From Greg at tekadence.net Fri Feb 1 03:59:14 2002 From: Greg at tekadence.net (Greg Deocampo) Date: Fri, 1 Feb 2002 00:59:14 -0800 Subject: [BiO BB] What is Pharmacogenomics ? In-Reply-To: Message-ID: <000001c1aafe$b9b449e0$28e9b3d1@tekadence> Here?s a great place to start: http://www.ornl.gov/hgmis/medicine/pharma.html /* /* Greg Deocampo /* CEO, Tekadence Incorporated /* 323 252 3863 /* /* "e pluribus unum" <-- "from many, one." /* -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Elsy Benjamin Sent: Thursday, January 31, 2002 3:26 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] What is Pharmacogenomics ? Hello Board Members, Could someone please explain the term pharmacogenomics and share their knowledge about the field? How can the modern information technology serve the pharmacogenomics? I would appreciate your views. Thank you. Regards Elsy -------------- next part -------------- An HTML attachment was scrubbed... URL: From Greg at tekadence.net Fri Feb 1 04:03:29 2002 From: Greg at tekadence.net (Greg Deocampo) Date: Fri, 1 Feb 2002 01:03:29 -0800 Subject: [BiO BB] What is Pharmacogenomics ? In-Reply-To: Message-ID: <000801c1aaff$51b540a0$28e9b3d1@tekadence> Here?s a great place to start: http://www.ornl.gov/hgmis/medicine/pharma.html /* /* Greg Deocampo /* CEO, Tekadence Incorporated /* 323 252 3863 /* /* "e pluribus unum" <-- "from many, one." /* -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Elsy Benjamin Sent: Thursday, January 31, 2002 3:26 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] What is Pharmacogenomics ? Hello Board Members, Could someone please explain the term pharmacogenomics and share their knowledge about the field? How can the modern information technology serve the pharmacogenomics? I would appreciate your views. Thank you. Regards Elsy -------------- next part -------------- An HTML attachment was scrubbed... URL: From browne.ken at virgin.net Fri Feb 1 04:21:01 2002 From: browne.ken at virgin.net (Ken Browne) Date: Fri, 1 Feb 2002 09:21:01 -0000 Subject: [BiO BB] What is Pharmacogenomics ? References: <000801c1aaff$51b540a0$28e9b3d1@tekadence> Message-ID: <000501c1ab17$e0e9c9e0$5890fea9@ken> Another good site is www.PharmacoGenomicsOnline.com as it has the latest news, events and a useful suppliers list. Cheers, Ken ----- Original Message ----- From: Greg Deocampo To: bio_bulletin_board at bioinformatics.org Sent: Friday, February 01, 2002 9:03 AM Subject: RE: [BiO BB] What is Pharmacogenomics ? Here?s a great place to start: http://www.ornl.gov/hgmis/medicine/pharma.html /* /* Greg Deocampo /* CEO, Tekadence Incorporated /* 323 252 3863 /* /* "e pluribus unum" <-- "from many, one." /* -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Elsy Benjamin Sent: Thursday, January 31, 2002 3:26 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] What is Pharmacogenomics ? Hello Board Members, Could someone please explain the term pharmacogenomics and share their knowledge about the field? How can the modern information technology serve the pharmacogenomics? I would appreciate your views. Thank you. Regards Elsy -------------- next part -------------- An HTML attachment was scrubbed... URL: From hz5 at njit.edu Sun Feb 3 12:40:32 2002 From: hz5 at njit.edu (hz5 at njit.edu) Date: Sun, 03 Feb 2002 12:40:32 -0500 (EST) Subject: [BiO BB] how to fetch sequences from web In-Reply-To: <20020124121740.18561.qmail@web14510.mail.yahoo.com> References: <20020124121740.18561.qmail@web14510.mail.yahoo.com> Message-ID: <1012758032.3c5d761015bb7@mailhost.njit.edu> I have put up a webtool that takes GenBank AccID's and the region of interest for the genes and retrieve all the sequence for you. For example, I want upstream 1000bp for the following genes: U69127 X64044 H45798 the tool will give back fasta format sequences with gi number of correponding contig as the description line. The sequence is retrived from NCBI from the draft contig sequence, not Genbank sequences. But in the result table, you have the link to Genbank sequences. The website is : http://130.219.130.104:8080/EZRetrieve/multirun.html Hope this will help. This is a new tool, I am sure there are many bugs in it, if anyone can help to evaluate and point out errors, I appreciate a lot. Thanks! Haibo Zhang Quoting Peri Suraj : > Hi group, > Do you know if there is any tool which can fetch > fasta formated sequences based on the accession > numbers list what i have with me. > I know that we can do this in GCG and EMBOSS. > I want a web based facility, because i do not have > access to EMBOSS or GCG. > Please reply soon ! > Thank you in advance > Suraj Peri > > ===== > PIL/CEBI/SDU/DK > > __________________________________________________ > Do You Yahoo!? > Great stuff seeking new owners in Yahoo! Auctions! > http://auctions.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Haibo Zhang Computational Biology, NJIT & Rutgers University http://afs13.njit.edu/~hz5 From hz5 at njit.edu Sun Feb 3 13:42:35 2002 From: hz5 at njit.edu (hz5 at njit.edu) Date: Sun, 03 Feb 2002 13:42:35 -0500 (EST) Subject: [BiO BB] sequence retrieval In-Reply-To: <1012758032.3c5d761015bb7@mailhost.njit.edu> References: <20020124121740.18561.qmail@web14510.mail.yahoo.com> <1012758032.3c5d761015bb7@mailhost.njit.edu> Message-ID: <1012761755.3c5d849bac4b3@mailhost.njit.edu> Hi group, I wrote a tool in java in order to retrieve any region of a gene from human genome draft sequence. The tool is like, say, I want -200 to +100 sequence of gene FUBP3(Genbank AccID is U69127), and the 300bp sequence will be retrieved.(upstream 200 and downstream 100) I also implement batch retrieve. The way I parse and retrieve is simply make a socket connection to NCBI and parse the webpage to get information, pages and tools involved are UniGene, LocusLink, and ASN.1 file. Questions and problems: 1. is there any biojave tool I can use here to make my tool compatible to biojava. I mean, I want to use biojava api to replace the same function in my code, because it is always a good idea to keep with the common source. 2. I am using contig to address the upstream and downstream sequences positions, this raise a problem when a gene is located at either end of the contig, I cannot find where is the information to tell what is the ajacent contig to this one. Say if a gene begins at position 20 on contig NT_001100, if I want upstream 200, I couldn't get it from this contig, I must know the contig that is overlap with this and retrive the sequence accordingly. But I currently don't know where this information is at NCBI. 3. I found that the contig that NCBI used for LocusLink is different in the contig they depict in the human genomic project draft report, any thought? 4. my class can also count atgcn composition and build random sequence according to the compostion; also can build first layer markov chain and build random sequence accordingly(tends to keep dimer composition). I used java Math.random(), is it safe? Are these tools already been implemented in biojava or they can be of some help? Any evaluation and suggestion are highly appreciated! Thanks! Haibo Zhang From rmp at sanger.ac.uk Sun Feb 3 14:23:44 2002 From: rmp at sanger.ac.uk (Roger Pettett) Date: Sun, 3 Feb 2002 19:23:44 +0000 (GMT) Subject: [BiO BB] sequence retrieval In-Reply-To: <1012761755.3c5d849bac4b3@mailhost.njit.edu> Message-ID: Have you looked at BioDAS? It sounds like you're duplicating effort as I'm pretty certain DAS does most of this for you. Check http://biodas.org/ Hope it helps, R. On Sun, 3 Feb 2002 hz5 at njit.edu wrote: > Hi group, > I wrote a tool in java in order to retrieve any region of a gene from human > genome draft sequence. > > The tool is like, say, I want -200 to +100 sequence of gene FUBP3(Genbank AccID > is U69127), and the 300bp sequence will be retrieved.(upstream 200 and > downstream 100) > > I also implement batch retrieve. The way I parse and retrieve is simply make a > socket connection to NCBI and parse the webpage to get information, pages and > tools involved are UniGene, LocusLink, and ASN.1 file. > > Questions and problems: > 1. is there any biojave tool I can use here to make my tool compatible to > biojava. I mean, I want to use biojava api to replace the same function in my > code, because it is always a good idea to keep with the common source. > 2. I am using contig to address the upstream and downstream sequences positions, > this raise a problem when a gene is located at either end of the contig, I > cannot find where is the information to tell what is the ajacent contig to this > one. Say if a gene begins at position 20 on contig NT_001100, if I want upstream > 200, I couldn't get it from this contig, I must know the contig that is overlap > with this and retrive the sequence accordingly. But I currently don't know where > this information is at NCBI. > 3. I found that the contig that NCBI used for LocusLink is different in the > contig they depict in the human genomic project draft report, any thought? > 4. my class can also count atgcn composition and build random sequence according > to the compostion; also can build first layer markov chain and build random > sequence accordingly(tends to keep dimer composition). I used java > Math.random(), is it safe? Are these tools already been implemented in biojava > or they can be of some help? > > Any evaluation and suggestion are highly appreciated! Thanks! > > Haibo Zhang > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- +---------------------------------------------------------------+ Roger Michael Pettett Email: rmp at sanger.ac.uk Project Leader (Web Systems), Web: http://www.sanger.ac.uk/ The Sanger Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SA +---------------------------------------------------------------+ From landman at scientificappliance.com Sun Feb 3 15:55:20 2002 From: landman at scientificappliance.com (Joe Landman) Date: 03 Feb 2002 15:55:20 -0500 Subject: [BiO BB] how to fetch sequences from web In-Reply-To: <1012758032.3c5d761015bb7@mailhost.njit.edu> References: <20020124121740.18561.qmail@web14510.mail.yahoo.com> <1012758032.3c5d761015bb7@mailhost.njit.edu> Message-ID: <1012769720.15122.14.camel@protein.dtw.macsch.com> I might suggest also looking at the NCBI Entrez site at http://www.ncbi.nlm.nih.gov/Entrez/ or batch Entrez at http://www.ncbi.nlm.nih.gov/entrez/batchentrez.cgi?db=Nucleotide For example, I used the accession BG938025 and put this into the search for text area. I selected nucleotide. I obtained a hit from the database, and changed the display from summary to FASTA and then clicked on the display button. You can also click on the save button to make a local copy. Batch Entrez lets you do basically the same thing, but with a set of accession numbers. Joe > Quoting Peri Suraj : > > > Hi group, > > Do you know if there is any tool which can fetch > > fasta formated sequences based on the accession > > numbers list what i have with me. > > I know that we can do this in GCG and EMBOSS. > > I want a web based facility, because i do not have > > access to EMBOSS or GCG. > > Please reply soon ! > > Thank you in advance > > Suraj Peri From amonida_zadissa at yahoo.se Sun Feb 3 20:18:31 2002 From: amonida_zadissa at yahoo.se (=?iso-8859-1?q?Amonida=20Zadissa?=) Date: Mon, 4 Feb 2002 02:18:31 +0100 (CET) Subject: FW: [BiO BB] how to fetch sequences from web Message-ID: <20020204011831.53433.qmail@web9507.mail.yahoo.com> Further comments on the NCBI Batch Entrez; unfortunately it does not always work depending on some error that has not yet been solved. One solution is using the main page of the NCBI, if you want to retrieve the sequences for many accession numbers. Just remember to separate the accession numbers by comma and then follow Joe's instructions for obtaining the sequences. Cheers, Amonida > I might suggest also looking at the NCBI Entrez site at > http://www.ncbi.nlm.nih.gov/Entrez/ or batch Entrez at > http://www.ncbi.nlm.nih.gov/entrez/batchentrez.cgi?db=Nucleotide > > > For example, I used the accession BG938025 and put this into > the search > for text area. I selected nucleotide. I obtained a hit from the > database, and changed the display from summary to FASTA and > then clicked > on the display button. You can also click on the save button > to make a > local copy. > > Batch Entrez lets you do basically the same thing, but with a set of > accession numbers. > > Joe > > > > > Quoting Peri Suraj : > > > > > Hi group, > > > Do you know if there is any tool which can fetch > > > fasta formated sequences based on the accession > > > numbers list what i have with me. > > > I know that we can do this in GCG and EMBOSS. > > > I want a web based facility, because i do not have > > > access to EMBOSS or GCG. > > > Please reply soon ! > > > Thank you in advance > > > Suraj Peri ===== --------------- Amonida Zadissa Otago University Dunedin New Zealand _____________________________________________________ Hitta sn?rapporter... fr?n 500 olika skidorter i Europa p? http://se.snow.yahoo.com From tmi0m0 at spi.power.uni-essen.de Mon Feb 4 04:56:47 2002 From: tmi0m0 at spi.power.uni-essen.de (=?iso-8859-1?Q?Johannes_H=FCsing?=) Date: Mon, 4 Feb 2002 10:56:47 +0100 Subject: [BiO BB] Retrieve list of GenBank Accession Numbers Message-ID: <20020204105647.14393@spi.power.uni-essen.de> Greetings, I would like to obtain a list of genes on a chromosome ordered by their pseudo base pair position. A list of this kind is supplied by the NCBI when you click on "Data as Table View" when in the Map Viewer. This gives me a list of genes with links. I would like to obtain the GenBank accession number which is listed under "Nucleotides" when you follow the respective link (if an accession number exists, which might not be the case for some ESTs). I wrote myself a Perl script to spider through these links and filter out the accession number. However, this causes a lot of Web traffic. Therefore, I'd like to know if such a list is already available. I have found something called gbgen.idx but this list seems to be dated. For example, you read about a gene named CHL1 in the gene list. When searching gbgen.idx, no appropriate PRI(mate) gene is found under this entry. Instead, the relevant accession number is listed under CALL. What I would like to know is: Is the list used by GenBank to select the gene names available somewhere? Sorry if this is unrelated to free software. I'd rather post general question like these in UseNet but haven't found an appropriate forum so far. Best wishes Johannes From bioinfo_india at yahoo.com Mon Feb 4 07:16:14 2002 From: bioinfo_india at yahoo.com (Peri Suraj) Date: Mon, 4 Feb 2002 04:16:14 -0800 (PST) Subject: [BiO BB] how to fetch sequences from web In-Reply-To: <3C501835.BB203BAF@bioinfo.weizmann.ac.il> Message-ID: <20020204121614.27119.qmail@web14508.mail.yahoo.com> Dear members, Batch Entrez is a good source and a powerful tool. But the only problem is difference in accession numbers. Consider a list of 500 sequences obtained from searching Mascot server ( Mass spec data) and all the seq. are reported on the basis of GI numbers. So if I submit all these GI to batch entrez i get ~600 sequences. So this GI adds redundancy to my retreived list. And the second problem is that the retrieved list will be jumbled. So this simple GI numbers some times add more work !So a inbuilt filter in BATCH ENTREZ will be a great tool ! cheers Suraj. ===== PIL/CEBI/SDU/DK __________________________________________________ Do You Yahoo!? Great stuff seeking new owners in Yahoo! Auctions! http://auctions.yahoo.com From finefeng at 163.com Tue Feb 5 10:26:49 2002 From: finefeng at 163.com (finefeng at 163.com) Date: Tue, 5 Feb 2002 23:26:49 +0800 Subject: [BiO BB] Medicine Development, Business Investment Message-ID: <200202051528.g15FS6T27914@www.bioinformatics.org> An HTML attachment was scrubbed... URL: From bioash at hotmail.com Tue Feb 5 12:49:59 2002 From: bioash at hotmail.com (Ashwin Sivakumar) Date: Tue, 05 Feb 2002 17:49:59 +0000 Subject: [BiO BB] C# in Bioinformatics? Message-ID: Hi group, I was wondering if any one has an idea on whether this language C# is being implemented for tool development by any corporate/research centers.Has anyone tested this language with respect to Bioinformatics tool development? regards, Ashwin ________________________________________________________________ Ashwin Sivakumar. Research Student, School of Biochemisty and Molecular Biology,Bioinformatics Group, University of Leeds,UK _________________________________________________________________ _________________________________________________________________ Chat with friends online, try MSN Messenger: http://messenger.msn.com From newgene at bigfoot.com Tue Feb 5 22:37:07 2002 From: newgene at bigfoot.com (NewGene) Date: Tue, 05 Feb 2002 21:37:07 -0600 Subject: [BiO BB] primer design program under windows Message-ID: <5.1.0.14.0.20020205213131.00b366c8@mail.uth.tmc.edu> Hi, group, I am looking for a primer design software which can run on windows platform and either support batch design for multiple sequences or be able to run as command line so that I can invoke it by script language. I downloaded primer3 source code, but I can not compile it successfully using bcc32.exe. Any suggestion from you are appreciated. Thanks. Chunlei From naitikkothari at india.com Wed Feb 6 03:48:50 2002 From: naitikkothari at india.com (Naitik Kothari) Date: Wed, 06 Feb 2002 13:48:50 +0500 Subject: [BiO BB] C# in Bioinformatics? [Powerful than Java] Message-ID: <20020206084851.16896.qmail@india.com> Hi Ashwin, C# is syntactically same as C++ (similar to Java). It is backed by Microsoft's .NET technology and has many advantages over Java. Graphics in C# is far better/faster than Java. It has the capability and extension of COM also. Currently none of the organization has announced usage of C# for its commercial development/research. May be some of the Research Institutes have started exploring that. Regards, Naitik N. Kothari Analyst (C++/Unix) Like exploring new technologies (C# is one of them) -----Original Message----- From: "Ashwin Sivakumar" Date: Tue, 05 Feb 2002 17:49:59 +0000 To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] C# in Bioinformatics? > > Hi group, > I was wondering if any one has an idea on whether this language C# is > being implemented for tool development by any corporate/research > centers.Has anyone tested this language with respect to > Bioinformatics tool development? > regards, > Ashwin > > > ________________________________________________________________ > Ashwin Sivakumar. > Research Student, > School of Biochemisty and Molecular Biology,Bioinformatics Group, > University of Leeds,UK -- _______________________________________________ Get your free email from http://mail.india.com From longli at itsa.ucsf.edu Sun Feb 10 03:44:03 2002 From: longli at itsa.ucsf.edu (Li, LC) Date: Sun, 10 Feb 2002 00:44:03 -0800 Subject: [BiO BB] primer design program under windows References: <5.1.0.14.0.20020205213131.00b366c8@mail.uth.tmc.edu> Message-ID: <000d01c1b20f$193f0aa0$52f7da80@long> Hi Chunlei, Primer3 can only run under Unix or Linux, you can not compile it in windows since it use unistd library. There is a solution to this problem. You can install Cygwin ( a unix envirnorment downloaded from redhat) in your windows, and compile using gcc which comes with Cygwin and do your command line primer design in Cygwin as well. Cygwin is very similar to your DOS console window, but actually it's Unix. If you have any question, just let me know. Longcheng Li ----- Original Message ----- From: NewGene To: Sent: Tuesday, February 05, 2002 7:37 PM Subject: [BiO BB] primer design program under windows > Hi, group, > I am looking for a primer design software which can run on > windows platform and either support batch design for multiple sequences or > be able to run as command line so that I can invoke it by script language. > I downloaded primer3 source code, but I can not compile it successfully > using bcc32.exe. > Any suggestion from you are appreciated. > > Thanks. > > > Chunlei > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From Sameer_Mohta at satyam.com Wed Feb 6 04:14:27 2002 From: Sameer_Mohta at satyam.com (Sameer_Mohta) Date: Wed, 6 Feb 2002 14:44:27 +0530 Subject: [BiO BB] primer design program under windows Message-ID: <877B003B6F03D511A22E00B0D078E7A8542B8B@hst.satyam.com> Hi Chulei, Though Primer3 is only available for Linux, you can still use it for Windows. You need to make one change in source code, hard code the value of MAX_PRIMER_LENGTH (primer3_main.c) and compile it using VC++. I think that will work. sameer -----Original Message----- From: Li, LC [mailto:longli at itsa.ucsf.edu] Sent: Sunday, February 10, 2002 2:14 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] primer design program under windows Hi Chunlei, Primer3 can only run under Unix or Linux, you can not compile it in windows since it use unistd library. There is a solution to this problem. You can install Cygwin ( a unix envirnorment downloaded from redhat) in your windows, and compile using gcc which comes with Cygwin and do your command line primer design in Cygwin as well. Cygwin is very similar to your DOS console window, but actually it's Unix. If you have any question, just let me know. Longcheng Li ----- Original Message ----- From: NewGene To: Sent: Tuesday, February 05, 2002 7:37 PM Subject: [BiO BB] primer design program under windows > Hi, group, > I am looking for a primer design software which can run on > windows platform and either support batch design for multiple sequences or > be able to run as command line so that I can invoke it by script language. > I downloaded primer3 source code, but I can not compile it successfully > using bcc32.exe. > Any suggestion from you are appreciated. > > Thanks. > > > Chunlei > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board ************************************************************************** This email (including any attachments) is intended for the sole use of the intended recipient/s and may contain material that is CONFIDENTIAL AND PRIVATE COMPANY INFORMATION. Any review or reliance by others or copying or distribution or forwarding of any or all of the contents in this message is STRICTLY PROHIBITED. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. ************************************************************************** From subba.raju at hbh.i-labs.ws Wed Feb 6 04:54:23 2002 From: subba.raju at hbh.i-labs.ws (Subba.Raju) Date: Wed, 6 Feb 2002 15:24:23 +0530 Subject: [BiO BB] (no subject) Message-ID: <759BC7ED1B0BD6118BC400B0D0E16A1F0FFDAA@BHILLS3NT002> Hello all, what is a Pattern and how is it different from Motif?? Is it true that all motifs are patterns but, not all patterns are motifs? cheers Subba From holeung at uclink.berkeley.edu Wed Feb 6 14:20:19 2002 From: holeung at uclink.berkeley.edu (Ho-Leung Ng) Date: Wed, 6 Feb 2002 11:20:19 -0800 Subject: [BiO BB] C# in Bioinformatics In-Reply-To: <200202061703.g16H3fT23257@www.bioinformatics.org> Message-ID: I and most other academic bioinformatics developers don't develop for Windows as a primary platform. I doubt you will see much impact of .NET or C# in academic bioinformatics centers. Ho-Leung Ng Univ. California, Berkeley From RMayreddy at NBME.org Wed Feb 6 14:31:24 2002 From: RMayreddy at NBME.org (Ravi Mayreddy) Date: Wed, 6 Feb 2002 14:31:24 -0500 Subject: [BiO BB] C# in Bioinformatics? [Powerful than Java] Message-ID: Hi: We would like to teach UNIX for a group of bioinformatics students. Any pointers to what to teach and any bioinformatics examples/exercises available? Thanks in advance! -Ravi -----Original Message----- From: Naitik Kothari [mailto:naitikkothari at india.com] Sent: Wednesday, February 06, 2002 3:49 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] C# in Bioinformatics? [Powerful than Java] Hi Ashwin, C# is syntactically same as C++ (similar to Java). It is backed by Microsoft's .NET technology and has many advantages over Java. Graphics in C# is far better/faster than Java. It has the capability and extension of COM also. Currently none of the organization has announced usage of C# for its commercial development/research. May be some of the Research Institutes have started exploring that. Regards, Naitik N. Kothari Analyst (C++/Unix) Like exploring new technologies (C# is one of them) -----Original Message----- From: "Ashwin Sivakumar" Date: Tue, 05 Feb 2002 17:49:59 +0000 To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] C# in Bioinformatics? > > Hi group, > I was wondering if any one has an idea on whether this language C# is > being implemented for tool development by any corporate/research > centers.Has anyone tested this language with respect to > Bioinformatics tool development? > regards, > Ashwin > > > ________________________________________________________________ > Ashwin Sivakumar. > Research Student, > School of Biochemisty and Molecular Biology,Bioinformatics Group, > University of Leeds,UK -- _______________________________________________ Get your free email from http://mail.india.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From blair.jennings at lionbioscience.com Wed Feb 6 14:54:43 2002 From: blair.jennings at lionbioscience.com (Blair Jennings) Date: Wed, 6 Feb 2002 11:54:43 -0800 Subject: [BiO BB] C# in Bioinformatics Message-ID: I would tend to disagree the Mono project which is porting C# to Unix; I believe will be a large influence in the adoption of .NET in all disciplines. For more info on Mono see: www.go-mono.com blair jennings Lion bioscience, Inc. -----Original Message----- From: Ho-Leung Ng [mailto:holeung at uclink.berkeley.edu] Sent: Wednesday, February 06, 2002 11:20 AM To: bio_bulletin_board at bioinformatics.org Cc: bioash at hotmail.com Subject: [BiO BB] C# in Bioinformatics I and most other academic bioinformatics developers don't develop for Windows as a primary platform. I doubt you will see much impact of .NET or C# in academic bioinformatics centers. Ho-Leung Ng Univ. California, Berkeley _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From dick at illumitek.com Wed Feb 6 16:04:28 2002 From: dick at illumitek.com (Dick Kirsch) Date: Wed, 6 Feb 2002 16:04:28 -0500 Subject: [BiO BB] In response to--C# in Bioinformatics? (Ashwin Sivakumar) Message-ID: <200202062109.g16L93W82339@illumi.vwh.net> An HTML attachment was scrubbed... URL: From rmp at sanger.ac.uk Wed Feb 6 16:43:00 2002 From: rmp at sanger.ac.uk (Roger Pettett) Date: Wed, 6 Feb 2002 21:43:00 +0000 (GMT) Subject: [BiO BB] C# in Bioinformatics? [no way!] In-Reply-To: Message-ID: On Wed, 6 Feb 2002, Ravi Mayreddy wrote: > Hi: > > We would like to teach UNIX for a group of bioinformatics students. Any > pointers to what to teach and any bioinformatics examples/exercises > available? > > Thanks in advance! UNIX-related - re: perl in bioinformatics I guess it would be fair to say perl exposes unix insides to a degree worthy of mention. IMHO It's probably worth teaching something at a slightly higher level than 'UNIX' for bioinformatics, and perl's a good place to start! :) http://bioperl.org/GetStarted/tpj_ls_bio.html R. -- +---------------------------------------------------------------+ Roger Michael Pettett Email: rmp at sanger.ac.uk Project Leader (Web Systems), Web: http://www.sanger.ac.uk/ The Sanger Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SA +---------------------------------------------------------------+ From burtonmatt at yahoo.com Wed Feb 6 21:26:25 2002 From: burtonmatt at yahoo.com (Matt) Date: Wed, 6 Feb 2002 21:26:25 -0500 Subject: [BiO BB] options for undergrads Message-ID: <15BDC0A8-1B72-11D6-9FAC-003065BFB0F2@yahoo.com> Hey I'm new to the board and have a question...I'm an undergrad in the US who's looking for a good place to study bioinformatics for a semester or two, like to look abroad, but I only speak english which might limit my options. Ideas? Any help you can give is greatly appreciated. matt _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com From Joel.Dudley at DevelopOnline.com Wed Feb 6 21:43:29 2002 From: Joel.Dudley at DevelopOnline.com (Joel Dudley) Date: Wed, 6 Feb 2002 19:43:29 -0700 Subject: [BiO BB] options for undergrads Message-ID: If you are looking abroad you can find opportunities in many European countries whose population speaks fluent English (Denmark, Holland, Finland, etc). If you are looking in the US then I am going to make a plug for my school, Arizona State. They offer two graduate options for those interested in Bioinformatics, but there is no dedicated bioinformatics undergraduate program. Also, the University of Arizona in Tuscon is a great place to study bioinformatics. Did I mention well over 300 days of sunshine here? :-). - joel -----Original Message----- From: Matt [mailto:burtonmatt at yahoo.com] Sent: Wednesday, February 06, 2002 7:26 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] options for undergrads Hey I'm new to the board and have a question...I'm an undergrad in the US who's looking for a good place to study bioinformatics for a semester or two, like to look abroad, but I only speak english which might limit my options. Ideas? Any help you can give is greatly appreciated. matt _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From prion at jhu.edu Wed Feb 6 21:44:07 2002 From: prion at jhu.edu (FREDERICK TAN) Date: Wed, 06 Feb 2002 21:44:07 -0500 Subject: [BiO BB] Genome Masking In-Reply-To: Message-ID: Good evening, . Could anyone comment on their experience masking entire genomes? I'm interested in trying to mask out general repeats in a genome of approximately 10^8 bases. I've noticed that RepeatMasker has libraries of known repeats for different organisms, but I'm interested in a general masking. . I came across one paper in Bioinformatics from Warren Gish's lab discussing MaskerAid, which supposedly has a 30-fold increase in speed at the most sensitive setting over the regular RepeatMasker. . Additionally, since it appears that the RepeatMasker web server at UW will only accept up to 100kb, a local installation of the software would be necessary. . Thanks in advance! Sincerely, Frederick Tan From swati_pande at hotmail.com Thu Feb 7 04:45:21 2002 From: swati_pande at hotmail.com (Swati Pande) Date: Thu, 07 Feb 2002 04:45:21 Subject: [BiO BB] Help with bioperl for Windows Message-ID: An HTML attachment was scrubbed... URL: From prion at jhu.edu Thu Feb 7 00:07:47 2002 From: prion at jhu.edu (FREDERICK TAN) Date: Thu, 07 Feb 2002 00:07:47 -0500 Subject: [BiO BB] options for undergrads In-Reply-To: <15BDC0A8-1B72-11D6-9FAC-003065BFB0F2@yahoo.com> Message-ID: . I don't know how comprehensive this list is, but it's fairly detailed, and is as good a place as any to start: http://www.iscb.org/univ.html Sincerely, Frederick Tan On Wed, 6 Feb 2002, Matt wrote: > Hey I'm new to the board and have a question...I'm an undergrad in the > US who's looking for a good place to study bioinformatics for a semester > or two, like to look abroad, but I only speak english which might limit From ayyagari.kiran at hbh.i-labs.ws Sat Feb 9 01:05:26 2002 From: ayyagari.kiran at hbh.i-labs.ws (Ayyagari.Kiran) Date: Sat, 9 Feb 2002 11:35:26 +0530 Subject: [BiO BB] whats a haplotype Message-ID: <759BC7ED1B0BD6118BC400B0D0E16A1F12158F@BHILLS3NT002> 1)can anyone tell me exactly what is a haplotype? ( is it just another strain of a species with haploid conditon?or results from a internal cross between two strains of any species) 2)how haplotypes are used in studying disease polymorphisms 3)how is it used in cytogenetics studies and genome Maps creation thanks A.S.Kiran i-labs From reillywu at yahoo.com Fri Feb 8 22:08:36 2002 From: reillywu at yahoo.com (Chunlei Wu) Date: Fri, 8 Feb 2002 19:08:36 -0800 (PST) Subject: [BiO BB] primer design program under windows In-Reply-To: <000d01c1b20f$193f0aa0$52f7da80@long> Message-ID: <20020209030836.67437.qmail@web20509.mail.yahoo.com> Thanks. I tried compiling under cygwin. It compiled successfully,but the executive file "primer3_core.exe" still doesn't work. Maybe I have to look for other tools. Chunlei --- "Li, LC" wrote: > Hi Chunlei, > > Primer3 can only run under Unix or Linux, you can > not compile it in windows > since it use unistd library. There is a solution to > this problem. You can > install Cygwin ( a unix envirnorment downloaded from > redhat) in your > windows, and compile using gcc which comes with > Cygwin and do your command > line primer design in Cygwin as well. Cygwin is very > similar to your DOS > console window, but actually it's Unix. > > If you have any question, just let me know. > > Longcheng Li > > ----- Original Message ----- > From: NewGene > To: > Sent: Tuesday, February 05, 2002 7:37 PM > Subject: [BiO BB] primer design program under > windows > > > > Hi, group, > > I am looking for a primer design > software which can run on > > windows platform and either support batch design > for multiple sequences or > > be able to run as command line so that I can > invoke it by script language. > > I downloaded primer3 source code, but I can not > compile it successfully > > using bcc32.exe. > > Any suggestion from you are > appreciated. > > > > Thanks. > > > > > > Chunlei > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board __________________________________________________ Do You Yahoo!? Send FREE Valentine eCards with Yahoo! Greetings! http://greetings.yahoo.com From micky at alum.mit.edu Thu Feb 7 23:44:24 2002 From: micky at alum.mit.edu (Michael Jastram) Date: Thu, 7 Feb 2002 23:44:24 -0500 Subject: [BiO BB] Iobion In-Reply-To: <00a201c1aa9c$82163c80$cba0b2d1@tekadence>; from Greg@tekadence.net on Thu, Jan 31, 2002 at 01:16:03PM -0800 References: <00a201c1aa9c$82163c80$cba0b2d1@tekadence> Message-ID: <20020207234424.B4410@capital.hamburg> There is a demo of their product, GeneTraffic, on their web site. Pretty slick, it's a server-based product with a Flash UI (Flash running inside Internet Explorer). It does Microarray analysis, using the chip image as the starting point. You can run standard analyses (dendogram, etc.). The system supports multiple users. And last, they claim to be MIAME compliant. I have no idea how well it scales (this is release 1.0), , but I must admit, I was impressed. I believe a single seat license is around $4000, and they do have academic discounts. Hope this helps. - Michael On Thu, Jan 31, 2002 at 01:16:03PM -0800, Greg Deocampo wrote: > > do you mean the company? > > > > [1]http://www.iobion.com/ > > > > G > > ----- Original Message ----- > > From: [2]Brat > > To: [3]bio_bulletin_board at bioinformatics.org > > Sent: Thursday, January 31, 2002 12:24 PM > > Subject: [BiO BB] Iobion > > Hi, > > > > Does anyone know anything about Iobion? > > References > > 1. http://www.iobion.com/ > 2. mailto:delmar_brat at hotmail.com > 3. mailto:bio_bulletin_board at bioinformatics.org -- _________________________ m i c h a e l jastram mailto:micky at alum.mit.edu w w w http://jastram.de _____PGP Fingerprint_____ 9301 1A1A 58C6 2433 4EA0 A040 A5AE 4122 12C1 EB80 From pajailwala at yahoo.com Sun Feb 10 12:27:03 2002 From: pajailwala at yahoo.com (Parthav Jailwala) Date: Sun, 10 Feb 2002 09:27:03 -0800 Subject: [BiO BB] whats a haplotype References: <759BC7ED1B0BD6118BC400B0D0E16A1F12158F@BHILLS3NT002> Message-ID: <001a01c1b258$2909aa50$e6986a8d@oemcomputer> hi in my view, the term 'haplotype' is just used to suggest a mix of phenotype and genotype information used to discover further insights into a problem. haplotypic data would suggest data inwhich the information content would contain both phenotypic data as well as genotypic data. I might be wrong, to wait for other views. thanks Parthav Jailwala Research Student Marquette University, WI ----- Original Message ----- From: "Ayyagari.Kiran" To: Sent: Friday, February 08, 2002 10:05 PM Subject: [BiO BB] whats a haplotype > 1)can anyone tell me exactly what is a haplotype? > ( is it just another strain of a species with haploid conditon?or results > from a internal cross between two strains of any species) > 2)how haplotypes are used in studying disease polymorphisms > 3)how is it used in cytogenetics studies and genome Maps creation > > thanks > > A.S.Kiran > i-labs > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com From hzi at uol.com.br Sun Feb 10 13:57:51 2002 From: hzi at uol.com.br (hzi at uol.com.br) Date: Sun, 10 Feb 2002 16:57:51 -0200 (BRST) Subject: [BiO BB] C# in Bioinformatics? In-Reply-To: References: Message-ID: <15462.49839.329745.30719@uol.com.br> Ashwin Sivakumar writes: > > Hi group, > I was wondering if any one has an idea on whether this language C# is > being implemented for tool development by any corporate/research > centers.Has anyone tested this language with respect to > Bioinformatics tool development? > regards, > Ashwin > > Dear Ashwin- It is my personal view that a proprietary language such as C# should not be used for research purposes, since it limits in a practical sense the applicability of new ideas and methods. Besides, from all the reviews I've read, C# is nothing but Microsoft's atempt to divert attention from JAVA, being a language with no substantial design inovation. Well, we've seen __that__ before... Regards, Henry synthespian at uol.com.br From dbeach at email.unc.edu Sun Feb 10 15:18:30 2002 From: dbeach at email.unc.edu (Dale Beach) Date: Sun, 10 Feb 2002 15:18:30 -0500 Subject: [BiO BB] whats a haplotype In-Reply-To: <001a01c1b258$2909aa50$e6986a8d@oemcomputer> References: <001a01c1b258$2909aa50$e6986a8d@oemcomputer> Message-ID: <72404922.1013354310@[192.168.1.101]> Carefull there- geneticists get rather irate when you confuse genotype and phenoptype. As a reminder, Genotype is the genetic composition of an organism. Phenotype is the outward expression or result of a genotype. For Mendel's peas as an example the genotypes WW and Ww would both produce round peas while ww would result in wrinkled peas. In this case the dominant W allele masks the presence of a recessive w allele. The haplotype is the genotype of the haploid or gamete stage of an organism's lifecycle. For most common animals this is hidden. Human egg and sperm do not have thier own lifecycle free of their parents, yet the gametes certainly have a genotype. In contrast budding yeast have a haploid lifecycle where the haplotype can be very important. If the recessive gene w for instance is required for the cell to live, then any haploid cell with only the w allele would be dead. If a diplod yeast of unknown genotype at the W locus is sporulated and dissected in such a way that each of the 4 resulting spores could be tested, then we could directly test the genotype of the diploid parent by assaying the haplotype of the progeny as follows: WW - all 4 spores live (W W W W) Ww - 2 spores live and 2 spores never grow (W W w w) ww - well we didn't need to worry its already dead! So in effect, when we can directly assay the haplotype we can more directly and rapidly assess the genotype of a diploid parent. In effect Parthav is correct, but the reasoning (at least for a geneticist) is much more resticted then his original post. I hope that this helps, and isn't too long of a reply. dale Dale Beach Department of Biology University of North Carolina Chapel Hill, NC --On Sunday, February 10, 2002 9:27 AM -0800 Parthav Jailwala wrote: > hi > in my view, the term 'haplotype' is just used to suggest a mix of > phenotype and genotype information used to discover further insights into > a problem. haplotypic data would suggest data inwhich the information > content would contain both phenotypic data as well as genotypic data. > I might be wrong, to wait for other views. > > thanks > Parthav Jailwala > Research Student > Marquette University, WI > ----- Original Message ----- > From: "Ayyagari.Kiran" > To: > Sent: Friday, February 08, 2002 10:05 PM > Subject: [BiO BB] whats a haplotype > > >> 1)can anyone tell me exactly what is a haplotype? >> ( is it just another strain of a species with haploid conditon?or > results >> from a internal cross between two strains of any species) >> 2)how haplotypes are used in studying disease polymorphisms >> 3)how is it used in cytogenetics studies and genome Maps creation >> >> thanks >> >> A.S.Kiran >> i-labs >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > _________________________________________________________ > Do You Yahoo!? > Get your free @yahoo.com address at http://mail.yahoo.com > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From blair.jennings at lionbioscience.com Mon Feb 11 11:52:12 2002 From: blair.jennings at lionbioscience.com (Blair Jennings) Date: Mon, 11 Feb 2002 08:52:12 -0800 Subject: [BiO BB] C# in Bioinformatics? Message-ID: I am sorry but C# is less a proprietary language than Java is. Until Java is released to a standards body like ECMA it will always be driven by proprietary concerns (i.e. SUN Microsystems and IBM). At least C# has been released to a standards body for approval which means everyone has a chance to say how it should evolve not just the select few that get appointed to a "Community process group". Blair Jennings Software Engineer Lion bioscience, Inc. -----Original Message----- From: hzi at uol.com.br [mailto:hzi at uol.com.br] Sent: Sunday, February 10, 2002 10:58 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] C# in Bioinformatics? Ashwin Sivakumar writes: > > Hi group, > I was wondering if any one has an idea on whether this language C# is > being implemented for tool development by any corporate/research > centers.Has anyone tested this language with respect to > Bioinformatics tool development? > regards, > Ashwin > > Dear Ashwin- It is my personal view that a proprietary language such as C# should not be used for research purposes, since it limits in a practical sense the applicability of new ideas and methods. Besides, from all the reviews I've read, C# is nothing but Microsoft's atempt to divert attention from JAVA, being a language with no substantial design inovation. Well, we've seen __that__ before... Regards, Henry synthespian at uol.com.br _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From Dan_Wiseman at idg.com Tue Feb 12 12:01:56 2002 From: Dan_Wiseman at idg.com (Dan_Wiseman at idg.com) Date: Tue, 12 Feb 2002 12:01:56 -0500 Subject: [BiO BB] Biocluster BOF at BioITWorld Conference & Expo Message-ID: <88256B5E.005E29E9.00@gcsmtp2.idg.com> J.W. Bizzaro, Chris Dagdigian and Andrew Fant will lead a Biocluster birds-of-a-feather session at BioITWorld Conference & Expo on Wednesday, March 13th at the World Trade Center Boston. This BOF is a networking and social gathering for anyone interested in the production use of linux clusters for life science informatics. BioITWorld Conference & Expo will take place March 12-14, 2002 at the World Trade Center Boston. Admission to the BOF session is FREE along with the exhibit hall floor, all keynote addresses and symposia. To attend the event with a free Discovery Pass, you must register at http://www.bioitworld.com using priority code: BORG01 (BORGzero-one) Members of the Bioinformatics.org may also receive a 25% discount off the conference packages by also using the priority code: BORG01. For more information, please visit http://www.bioitworld.com From hz5 at njit.edu Wed Feb 13 11:24:24 2002 From: hz5 at njit.edu (hz5 at njit.edu) Date: Wed, 13 Feb 2002 11:24:24 -0500 (EST) Subject: [BiO BB] primer design program under windows In-Reply-To: <5.1.0.14.0.20020205213131.00b366c8@mail.uth.tmc.edu> References: <5.1.0.14.0.20020205213131.00b366c8@mail.uth.tmc.edu> Message-ID: <1013617464.3c6a93384baa2@mailhost.njit.edu> Hi, this paper might help: http://nar.oupjournals.org/cgi/content/full/29/21/4373?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1013617301792_2443&stored_search=&FIRSTINDEX=0&sortspec=Score+desc+PUBDATE_SORTDATE+desc&volume=29&firstpage=4373&journalcode=nar NAR 2001 vol. 29 No. 21 4373-4377 Haibo Zhang Quoting NewGene : > Hi, group, > I am looking for a primer design software which can run on > > windows platform and either support batch design for multiple sequences > or > be able to run as command line so that I can invoke it by script > language. > I downloaded primer3 source code, but I can not compile it successfully > > using bcc32.exe. > Any suggestion from you are appreciated. > > Thanks. > > > Chunlei > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Haibo Zhang Computational Biology, NJIT & Rutgers University http://afs13.njit.edu/~hz5 From Manoj_Kenkare at frost.com Thu Feb 14 02:00:40 2002 From: Manoj_Kenkare at frost.com (Manoj Kenkare) Date: Thu, 14 Feb 2002 01:00:40 -0600 Subject: [BiO BB] Manoj Kenkare is out of the office. Message-ID: I will be out of the office starting 02/11/2002 and will not return until 02/15/2002. I will respond to your message when I return. I will be checking my voicemail during my travel. If you have an urgent matter please leave me a message. My direct number is 210-247-2443. From ebowen99 at ivillage.com Thu Feb 14 20:09:57 2002 From: ebowen99 at ivillage.com (Elizabeth Bowen) Date: 14 Feb 2002 17:09:57 -0800 Subject: [BiO BB] whats a haplotype Message-ID: <20020215010957.8753.cpmta@c006.snv.cp.net> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From lu_guoqing at hotmail.com Thu Feb 14 21:15:18 2002 From: lu_guoqing at hotmail.com (Guoqing) Date: Thu, 14 Feb 2002 21:15:18 -0500 Subject: [BiO BB] link Access database to GenBank Message-ID: Hi group, We are constructing a Ms Access database. There are tables which have a column named GenBank accession number. I want to know whether I can do the following steps to add columns with info from GenBank: 1) get GenBank accession number from the database 2) retrieve DNA sequences or amino acid sequences with the accession number; 3) add one column or more in the table and store retrieved sequences. Are there any tools which can be used for such a purpose? If i want to develop such a program is it difficult? Any suggestion will be appreciated. Best regards, Guoqing -------------- next part -------------- An HTML attachment was scrubbed... URL: From gow_geek at yahoo.com Fri Feb 15 12:29:51 2002 From: gow_geek at yahoo.com (gowtham ramasamy) Date: Fri, 15 Feb 2002 09:29:51 -0800 (PST) Subject: [BiO BB] (no subject) Message-ID: <20020215172951.70533.qmail@web13004.mail.yahoo.com> hi group im trying to use modeller for predicting 3d structures of protein. if any one of u used to it let me know it. i would like to clarify my some doubts regards gowtham __________________________________________________ Do You Yahoo!? Got something to say? Say it better with Yahoo! Video Mail http://mail.yahoo.com From rbrinkman at xenongenetics.com Fri Feb 15 14:29:39 2002 From: rbrinkman at xenongenetics.com (Ryan Brinkman) Date: Fri, 15 Feb 2002 11:29:39 -0800 Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #198 - 2 msgs Message-ID: you should look at Ensembl and BioPerl. You can pull out all the sequences you want given a ID using Ensembl's MySQL database (either installed locally or accessed remotly through either SQL or PERl API calls). >We are constructing a Ms Access database. There are tables which have a = >column named GenBank accession number. I want to know whether I can do = >the following steps to add columns with info from GenBank: 1) get = >GenBank accession number from the database 2) retrieve DNA sequences or = >amino acid sequences with the accession number; 3) add one column or = >more in the table and store retrieved sequences. Are there any tools = >which can be used for such a purpose? If i want to develop such a = >program is it difficult? Any suggestion will be appreciated. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stuartcraigie at hotmail.com Mon Feb 18 13:53:02 2002 From: stuartcraigie at hotmail.com (stuart craigie) Date: Mon, 18 Feb 2002 18:53:02 +0000 Subject: [BiO BB] Student Seeks Bioinformatics Dissertation Placement Message-ID: I am currently studying for an Mres in Bioinformatics at the University of Glasgow, Scotland. As part of our course requirement we are to organise a 15-week (summer) industrial placement with a company. As an undergraduate, I attained a (2:1) in Pharmacology. As well as this, I also carried out a funded summer research project with the Wellcome Trust, which I applied for on a competitive basis. Both the above project and my honours project were CNS related. During my course in Bioinformatics I have had extensive programming experience in Java, gained familiarity with various Unix based Bioinformatics software (GCG). I will shortly be learning Oracle based database management and also how to program simple scripts in Perl as well as CGI programming. The course contains a biology strand, which covers genomic analysis and functional genomics, molecular graphics, microarray technology and protein structure, folding and prediction. Please get in touch if you can help. Thanks, Stuart _________________________________________________________________ Join the world?s largest e-mail service with MSN Hotmail. http://www.hotmail.com From Sameer_Mohta at satyam.com Tue Feb 19 01:40:37 2002 From: Sameer_Mohta at satyam.com (Sameer_Mohta) Date: Tue, 19 Feb 2002 12:10:37 +0530 Subject: [BiO BB] sequence retrieval Message-ID: <877B003B6F03D511A22E00B0D078E7A8542C0E@HSTNT001> Hi, i have a small query regarding BIoDAS.As Haibo Zhang asked about retreiving information of a particular gene, and you suggested that BioDAS can serve the purpose. But my question is that BioDAS server has to be up on the specified server for that. or is it possible to reteive information without BioDAS server. b'coz as far as my knowledge is concerned, BioDAS is running on TIGR, Ensembl, Flybase and 2-3 other sites. thanks sameer -----Original Message----- From: Roger Pettett [mailto:rmp at sanger.ac.uk] Sent: Monday, February 04, 2002 12:54 AM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] sequence retrieval Have you looked at BioDAS? It sounds like you're duplicating effort as I'm pretty certain DAS does most of this for you. Check http://biodas.org/ Hope it helps, R. On Sun, 3 Feb 2002 hz5 at njit.edu wrote: > Hi group, > I wrote a tool in java in order to retrieve any region of a gene from human > genome draft sequence. > > The tool is like, say, I want -200 to +100 sequence of gene FUBP3(Genbank AccID > is U69127), and the 300bp sequence will be retrieved.(upstream 200 and > downstream 100) > > I also implement batch retrieve. The way I parse and retrieve is simply make a > socket connection to NCBI and parse the webpage to get information, pages and > tools involved are UniGene, LocusLink, and ASN.1 file. > > Questions and problems: > 1. is there any biojave tool I can use here to make my tool compatible to > biojava. I mean, I want to use biojava api to replace the same function in my > code, because it is always a good idea to keep with the common source. > 2. I am using contig to address the upstream and downstream sequences positions, > this raise a problem when a gene is located at either end of the contig, I > cannot find where is the information to tell what is the ajacent contig to this > one. Say if a gene begins at position 20 on contig NT_001100, if I want upstream > 200, I couldn't get it from this contig, I must know the contig that is overlap > with this and retrive the sequence accordingly. But I currently don't know where > this information is at NCBI. > 3. I found that the contig that NCBI used for LocusLink is different in the > contig they depict in the human genomic project draft report, any thought? > 4. my class can also count atgcn composition and build random sequence according > to the compostion; also can build first layer markov chain and build random > sequence accordingly(tends to keep dimer composition). I used java > Math.random(), is it safe? Are these tools already been implemented in biojava > or they can be of some help? > > Any evaluation and suggestion are highly appreciated! Thanks! > > Haibo Zhang > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- +---------------------------------------------------------------+ Roger Michael Pettett Email: rmp at sanger.ac.uk Project Leader (Web Systems), Web: http://www.sanger.ac.uk/ The Sanger Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SA +---------------------------------------------------------------+ _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board ************************************************************************** This email (including any attachments) is intended for the sole use of the intended recipient/s and may contain material that is CONFIDENTIAL AND PRIVATE COMPANY INFORMATION. Any review or reliance by others or copying or distribution or forwarding of any or all of the contents in this message is STRICTLY PROHIBITED. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. ************************************************************************** From newgene at bigfoot.com Tue Feb 19 16:03:06 2002 From: newgene at bigfoot.com (NewGene) Date: Tue, 19 Feb 2002 15:03:06 -0600 Subject: [BiO BB] restrict the blast result by e-value? Message-ID: <5.1.0.14.0.20020219144814.00b37738@mail.uth.tmc.edu> Hi, group, If I do a blast search and want only hits with 100% identity between query and subject, how can I specify the e-value or other parameters for this purpose? I am not familiar with the underlying statistics of Blast, but it seems that the query sequences with same length have the same e-values for perfect match. If there is a formula available to predict this e-value, it will help to put it into scripts run my localblast automatically using any length sequence. Thanks in advance for your help. CL From prion at jhu.edu Wed Feb 20 00:31:03 2002 From: prion at jhu.edu (FREDERICK TAN) Date: Wed, 20 Feb 2002 00:31:03 -0500 Subject: [BiO BB] restrict the blast result by e-value? In-Reply-To: <5.1.0.14.0.20020219144814.00b37738@mail.uth.tmc.edu> Message-ID: . So let me start out an answer like any good one should, with a reference: http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html This is from the NCBI's site, which has a *lot* of educational links about various aspects of that side in computational biology. . That link is I feel fairly non-technical, with as few equations as possible, yet still retaining a good amount of specific details. If you want the more mathematically rigorous explanations, search for papers by Altschul, Lipman, Gish, Waterson, Karlin, Pearson, etc. as they've done a lot of important work in this area. . But to quickly answer your questions on e-values: the score you get is dependent upon the length and complexity of the query sequence, as well as the size of the database. It's generally not a good measure to examine matches by only looking at the percent identity. I believe that the past few iterations of Blast have been using P-scores instead of E-values-- which are essentially the same when the values are significant enough. And the p-values are interpreted as: the probability that this match could occur by chance. . And on selecting a return threshold: I don't remember an option on the web server for that. There is an e-value cutoff (in the most general case, I'll believe scores of e-20 or greater), but again, it doesn't necessarily flow that 100% identity == great e-value. Sincerely, Frederick Tan PS. Note that for the most accurate definitions, go to the references On Tue, 19 Feb 2002, NewGene wrote: > If I do a blast search and want only hits with 100% identity > between query and subject, how can I specify the e-value or other > parameters for this purpose? I am not familiar with the underlying From kiran_ayyagari at yahoo.com Wed Feb 20 05:48:00 2002 From: kiran_ayyagari at yahoo.com (Ayyagari Kiran) Date: Wed, 20 Feb 2002 02:48:00 -0800 (PST) Subject: [BiO BB] what is the minimum length of protein? and why differentiate protein & peptides Message-ID: <20020220104800.3579.qmail@web11906.mail.yahoo.com> hi, 1)what is the minimu length of A protein ? (please mention the minimal possible length of protein, its minimal mol wt(in kDa) and also types of proteins by example. 2) is it that a biomolecule can be called as a protein based on its structural organization (like if domains are present) or is it that a biomolecule can be called as protein based on Functional implications??like example can be toxin of 55 amino acids causes raise in antibodies production. why is it not called a protein and why it is called a peptide toxin despite having amino acids. thanks in advance A.S.Kiran __________________________________________________ Do You Yahoo!? Yahoo! Sports - Coverage of the 2002 Olympic Games http://sports.yahoo.com From hinaishadh at netscape.net Wed Feb 20 13:15:45 2002 From: hinaishadh at netscape.net (hinaishadh at netscape.net) Date: Wed, 20 Feb 2002 13:15:45 -0500 Subject: [BiO BB] Definition of a protein Message-ID: <7F036E6C.7A78E91D.0F2DE52D@netscape.net> Hi Kiran, I am sure I will get a lot of flake for this BUT Amino acids are building blocks of protein. In other words proteins are polymers of amino acids. How many? By definition 2 or more should do. That said, keep in mind that earlier biochemical scientists did not know the nature of the molecule thay were working on. So, the names like toxins, or even "active principle" in the ddays of Pasteur and Robert Koch (1870s!). To further complicate matters you have glycoproteins that are mainly proteins with sugar side chains, and peptidoglycans that have small peptide backbone but really long, branched sugars chains (generally constituting 90% of the mol. wt. of the whole molecule). LOts of work was done using precipitation as one way to isolate large biological molecules. So the growth factors and small peptides that were soluble by such criteria were not called proteins but peptides or peptide hormones etc. Hope this helps Naishadh Desai Perlegen Sciences Mountain View, CA 94043 > >Message: 3 >Date: Wed, 20 Feb 2002 02:48:00 -0800 (PST) >From: Ayyagari Kiran >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] what is the minimum length of protein? and why differentiate protein & peptides >Reply-To: bio_bulletin_board at bioinformatics.org > >hi, >1)what is the minimu length of A protein ? >(please mention the minimal possible length of >protein, its minimal mol wt(in kDa) and also types of >proteins by example. > >2) is it that a biomolecule can be called as a protein >based on its structural organization (like if domains >are present) >or >is it that a biomolecule can be called as protein >based on Functional implications??like example can be >toxin of 55 amino acids causes raise in antibodies >production. why is it not called a protein and why it >is called a peptide toxin despite having amino acids. > >thanks in advance > >A.S.Kiran > > >__________________________________________________ >Do You Yahoo!? >Yahoo! Sports - Coverage of the 2002 Olympic Games >http://sports.yahoo.com > > >--__--__-- > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > >End of BiO_Bulletin_Board Digest > -- __________________________________________________________________ Your favorite stores, helpful shopping tools and great gift ideas. Experience the convenience of buying online with Shop at Netscape! http://shopnow.netscape.com/ Get your own FREE, personal Netscape Mail account today at http://webmail.netscape.com/ From r_senthil19 at yahoo.com Fri Feb 22 00:42:00 2002 From: r_senthil19 at yahoo.com (senthil kumar) Date: Thu, 21 Feb 2002 21:42:00 -0800 (PST) Subject: [BiO BB] hi! Message-ID: <20020222054200.61139.qmail@web13208.mail.yahoo.com> hi groupz, i am a s/w engineer in c++/vc++/java platform. i have ineterst in DNA molecular biology.i would like to develop useful tool for bioinformatics. pls suggest and guide a good project since i am new to this field.this will be a open source project . luv, senthil __________________________________________________ Do You Yahoo!? Yahoo! Sports - Coverage of the 2002 Olympic Games http://sports.yahoo.com From MitchellA at nu.ac.za Fri Feb 22 01:44:29 2002 From: MitchellA at nu.ac.za (Andrew Mitchell) Date: Fri, 22 Feb 2002 08:44:29 +0200 Subject: [BiO BB] Re: Definition of a protein Message-ID: Proteins are polypeptides. Peptides are short chains of amino acids. Just how long can a peptide be before it should be called a protein? I'm not going to stick my neck out a give a number, but one thing is clear: 2 amino acids does not a protein make. Andrew =============================================================== Andrew Mitchell Senior Lecturer, Molecular Phylogenetics School of Molecular and Cellular Biosciences University of Natal Private Bag X01 Scottsville, 3209 SOUTH AFRICA Tel: +27 (0)33 260 5815 Fax: +27 (0)33 260 5462 http://www.nu.ac.za/department/members/members.asp?dept=bioscienunp&id=123456 >>> bio_bulletin_board-request at bioinformatics.org 02/02/21 07:02:18 >>> Message: 1 Date: Wed, 20 Feb 2002 13:15:45 -0500 From: hinaishadh at netscape.net To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Definition of a protein Reply-To: bio_bulletin_board at bioinformatics.org Hi Kiran, I am sure I will get a lot of flake for this BUT Amino acids are building blocks of protein. In other words proteins are polymers of amino acids. How many? By definition 2 or more should do. That said, keep in mind that earlier biochemical scientists did not know the nature of the molecule thay were working on. So, the names like toxins, or even "active principle" in the ddays of Pasteur and Robert Koch (1870s!). To further complicate matters you have glycoproteins that are mainly proteins with sugar side chains, and peptidoglycans that have small peptide backbone but really long, branched sugars chains (generally constituting 90% of the mol. wt. of the whole molecule). LOts of work was done using precipitation as one way to isolate large biological molecules. So the growth factors and small peptides that were soluble by such criteria were not called proteins but peptides or peptide hormones etc. Hope this helps Naishadh Desai Perlegen Sciences Mountain View, CA 94043 > >Message: 3 >Date: Wed, 20 Feb 2002 02:48:00 -0800 (PST) >From: Ayyagari Kiran >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] what is the minimum length of protein? and why differentiate protein & peptides >Reply-To: bio_bulletin_board at bioinformatics.org > >hi, >1)what is the minimu length of A protein ? >(please mention the minimal possible length of >protein, its minimal mol wt(in kDa) and also types of >proteins by example. > >2) is it that a biomolecule can be called as a protein >based on its structural organization (like if domains >are present) >or >is it that a biomolecule can be called as protein >based on Functional implications??like example can be >toxin of 55 amino acids causes raise in antibodies >production. why is it not called a protein and why it >is called a peptide toxin despite having amino acids. > >thanks in advance > >A.S.Kiran > -------------- next part -------------- An HTML attachment was scrubbed... URL: From chapmanb at arches.uga.edu Fri Feb 22 07:21:35 2002 From: chapmanb at arches.uga.edu (Brad Chapman) Date: Fri, 22 Feb 2002 07:21:35 -0500 Subject: [BiO BB] Following the Biohackathon Message-ID: <20020222072135.A25305@ci350185-a.athen1.ga.home.com> [Apologies for the cross-posting. I know, I get 10 copies of this message too.] Hello all; As many of you may know, quite a few people involved with the open-bio projects (http://www.open-bio.org/) are participating in a two-part hackathon, sponsored by the nice folks at O'Reilly and Electric Genetics. This hackathon gives the motley crew involved with various open source bioinformatics projects (ie. BioPerl, BioJava, Biopython, DAS, Ensembl, BioRuby, GO, MOBY, OmniGene...) a chance to get together and get some serious hacking done. The first part took place at the O'Reilly Bioinformatics Conference in Tucson during the end of January. Due to the fact that all of us involved are hard working and smarter than your average bear, we accomplished quite a bit of good stuff and were very proud of ourselves. Big pats on the back all around. This mail is to let you know that the second part of the hackathon will be taking place next week in Cape Town, South Africa. You can find tons of detail about the schedule and plans on the Electric Genetics website: http://www.egenetics.com/?Section=Biohackathon_details&Parent=open_source If you're keen to follow the exciting world of open-source bioinformatics hacking play-by-play, we'll be fully on-line at: http://www.technophage.com This page will feature technical details of what we're working on, amazing pictures of South Africa, and color commentary featuring all of those nasty tidbits you've always wanted to hear about your favorite bioinformatics programmer. Although-there-certainly-won't-be-anything-juicy-about-me-ly yr's, Brad -- PGP public key available from http://pgp.mit.edu/ From mkgovindis at yahoo.com Mon Feb 25 00:55:07 2002 From: mkgovindis at yahoo.com (govind mk) Date: Sun, 24 Feb 2002 21:55:07 -0800 (PST) Subject: [BiO BB] Emboss help Message-ID: <20020225055507.25326.qmail@web12906.mail.yahoo.com> Hello users I am using Emboss program Showalign which displays a mulitple sequence alignment in a user friendly format. I get symbols "x" and "X" in the alignment consensus line . I am unable to differentiate these upper and lower case letters. Can some one help me out ? Thank you. -Govind --------------------------------- Do You Yahoo!? Yahoo! Sports - Coverage of the 2002 Olympic Games -------------- next part -------------- An HTML attachment was scrubbed... URL: From selonline at hotmail.com Tue Feb 26 07:29:51 2002 From: selonline at hotmail.com (selvi subramanian) Date: Tue, 26 Feb 2002 17:59:51 +0530 Subject: [BiO BB] Emboss help Message-ID: well i believe the conservative replacements are denoted by x and the non conservative as X, govind!!! S:) >From: govind mk >Reply-To: bio_bulletin_board at bioinformatics.org >To: bio_bulletin_board at bioinformatics.org >Subject: [BiO BB] Emboss help >Date: Sun, 24 Feb 2002 21:55:07 -0800 (PST) > > >Hello users > >I am using Emboss program Showalign which displays a mulitple sequence >alignment in a user friendly format. > >I get symbols "x" and "X" in the alignment consensus line . I am unable to >differentiate these upper and lower case letters. > >Can some one help me out ? > >Thank you. > >-Govind > > > >--------------------------------- >Do You Yahoo!? >Yahoo! Sports - Coverage of the 2002 Olympic Games _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp. From mkgovindis at yahoo.com Tue Feb 26 22:07:06 2002 From: mkgovindis at yahoo.com (govind mk) Date: Tue, 26 Feb 2002 19:07:06 -0800 (PST) Subject: [BiO BB] Emboss help In-Reply-To: Message-ID: <20020227030706.14290.qmail@web12903.mail.yahoo.com> Hello users, This email is from the person who has written the program Showalign ... The uppercase consensus symbols is meant to indicate that the consensus is strong and lowercase indicates that it is weak. In practice, I don't really like this feature and genarally turn it off. The cutoff for setting the case of the consensus is set by the qualifier '-setcase'. If the score of the matches is above this value, then the symbol is in uppercase, iot the score is below the -setcase value then the symbol is in lowercase. To put all of the consensus symbols into uppercase or lowercase, make -setcase very low (-100000 ?) or very large (100000 ?) Regards, Gary _Govind selvi subramanian wrote: well i believe the conservative replacements are denoted by x and the non conservative as X, govind!!! S:) --------------------------------- Do You Yahoo!? Yahoo! Greetings - Send FREE e-cards for every occasion! -------------- next part -------------- An HTML attachment was scrubbed... URL: