From kiekyon.huang at gmail.com Fri Oct 2 20:29:13 2009 From: kiekyon.huang at gmail.com (Kie Kyon Huang) Date: Sat, 3 Oct 2009 08:29:13 +0800 Subject: [BiO BB] gff to sequence Message-ID: Hi, Is there a way to quickly extract out the coordinates from a gff file and the corresponding sequence from a fasta file? thanks From dan.bolser at gmail.com Sat Oct 3 07:54:51 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Sat, 3 Oct 2009 12:54:51 +0100 Subject: [BiO BB] gff to sequence In-Reply-To: References: Message-ID: <2c8757af0910030454t454facf1r1d083120aec1e41@mail.gmail.com> You can do this easily in Perl... Here is some 'pseudo code' to (roughly) do it... ## Get a hash of sequences, keys = IDs, values = sequence strings; my %sequences; ... # open the GFF file ... while(my $gff = ){ my @gffcols = split(/\t/, $gff); print substr($sequence{$gffcols[0]}, $gffcols[3], $gffcols[4] - $gffcols[3]), "\n"; ... } Or something roughly similar to the above ;-) Dan. 2009/10/3 Kie Kyon Huang : > Hi, > > Is there a way to quickly extract out the coordinates from a gff file > and the corresponding sequence from a fasta file? > > thanks > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From marchywka at hotmail.com Sat Oct 3 08:59:10 2009 From: marchywka at hotmail.com (Mike Marchywka) Date: Sat, 3 Oct 2009 08:59:10 -0400 Subject: [BiO BB] gff to sequence In-Reply-To: <2c8757af0910030454t454facf1r1d083120aec1e41@mail.gmail.com> References: Message-ID: <2c8757af0910030454t454facf1r1d083120aec1e41 at mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 ---------------------------------------- > Date: Sat=2C 3 Oct 2009 12:54:51 +0100 > From: dan.bolser at gmail.com > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] gff to sequence > > You can do this easily in Perl... Here is some 'pseudo code' to > (roughly) do it... > > > ## Get a hash of sequences=2C keys =3D IDs=2C values =3D sequence strings= =3B > my %sequences=3B > ... > > # open the GFF file ... > > while(my $gff =3D ){ > my @gffcols =3D split(/\t/=2C $gff)=3B > > print substr($sequence{$gffcols[0]}=2C $gffcols[3]=2C $gffcols[4] - > $gffcols[3])=2C "\n"=3B > ... > } > > > Or something roughly similar to the above =3B-) > > Dan. > > > 2009/10/3 Kie Kyon Huang : >> Hi=2C >> >> Is there a way to quickly extract out the coordinates from a gff file >> and the corresponding sequence from a fasta file? >> I guess it depends what you mean by quick- quick to write you could use awk but then it depends what additional things you want to do with results.=20 I ended up writing a C++ fasta utility program since PERL can slow down som= etimes but I ended up grabbing a couple of regex libraries to let me=20 grep names etc.=20 =0A= _________________________________________________________________=0A= Hotmail: Free=2C trusted and rich email service.=0A= http://clk.atdmt.com/GBL/go/171222984/direct/01/= From leo.goodstadt at dpag.ox.ac.uk Sat Oct 3 09:14:51 2009 From: leo.goodstadt at dpag.ox.ac.uk (Leo Goodstadt) Date: Sat, 3 Oct 2009 14:14:51 +0100 Subject: [BiO BB] gff to sequence In-Reply-To: References: Message-ID: <55D5E770D835674587C89EE6239C5DAE1D4FFF4518@EXMBX06.ad.oak.ox.ac.uk> > >> Is there a way to quickly extract out the coordinates from a gff file > >> and the corresponding sequence from a fasta file? > >> > This seems of such general use that it begs a small utility which will take a (possibly indexed) fasta file, a gff and output the sequences you want. What would people want from such a programme? Is GTF (http://mblab.wustl.edu/GTF2.html) more useful or GFF? Would different elements from the same group (gene/transcript) be joined together in order? Would one want filtering on the "features" column so one could retrieve all splice sites or codon exons? What would be the output? Another fasta file? How would each "group" of Sequences (e.g. transcript) be labelled? By a user supplied regular expression? > I guess it depends what you mean by quick- quick to write you could use awk > but then it depends what additional things you want to do with results.=20 > I ended up writing a C++ fasta utility program since PERL can slow down som= > etimes but I ended up grabbing a couple of regex libraries to let me=20 > grep names etc.=20 I hoped you used boost:regex which will be in the next c++ standard (http://www.boost.org/doc/libs/1_40_0/libs/regex/doc/html/index.html) and is as easy to use and powerful as perl/python regular expressions (though c rules on escaping backslashes are a pain). Leo Leo Goodstadt From jgbaum at gmail.com Sat Oct 3 13:02:48 2009 From: jgbaum at gmail.com (J Greenbaum) Date: Sat, 3 Oct 2009 10:02:48 -0700 Subject: [BiO BB] gff to sequence In-Reply-To: References: <2c8757af0910030454t454facf1r1d083120aec1e41@mail.gmail.com> Message-ID: <701a2c50910031002v428eecd5ye306a4ce95b02156@mail.gmail.com> I would suggest using the bioperl modules for parsing GFF and FASTA files: Bio::Tools::GFF and Bio::SeqIO This should save you a lot of pain. -Jason On Sat, Oct 3, 2009 at 5:59 AM, Mike Marchywka wrote: > > <2c8757af0910030454t454facf1r1d083120aec1e41 at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > MIME-Version: 1.0 > > > > > > > > > > > ---------------------------------------- > > Date: Sat=2C 3 Oct 2009 12:54:51 +0100 > > From: dan.bolser at gmail.com > > To: bbb at bioinformatics.org > > Subject: Re: [BiO BB] gff to sequence > > > > You can do this easily in Perl... Here is some 'pseudo code' to > > (roughly) do it... > > > > > > ## Get a hash of sequences=2C keys =3D IDs=2C values =3D sequence > strings= > =3B > > my %sequences=3B > > ... > > > > # open the GFF file ... > > > > while(my $gff =3D ){ > > my @gffcols =3D split(/\t/=2C $gff)=3B > > > > print substr($sequence{$gffcols[0]}=2C $gffcols[3]=2C $gffcols[4] - > > $gffcols[3])=2C "\n"=3B > > ... > > } > > > > > > Or something roughly similar to the above =3B-) > > > > Dan. > > > > > > 2009/10/3 Kie Kyon Huang : > >> Hi=2C > >> > >> Is there a way to quickly extract out the coordinates from a gff file > >> and the corresponding sequence from a fasta file? > >> > > I guess it depends what you mean by quick- quick to write you could use awk > but then it depends what additional things you want to do with results.=20 > I ended up writing a C++ fasta utility program since PERL can slow down > som= > etimes but I ended up grabbing a couple of regex libraries to let me=20 > grep names etc.=20 > > > > > =0A= > _________________________________________________________________=0A= > Hotmail: Free=2C trusted and rich email service.=0A= > http://clk.atdmt.com/GBL/go/171222984/direct/01/= > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From marchywka at hotmail.com Sat Oct 3 19:06:05 2009 From: marchywka at hotmail.com (Mike Marchywka) Date: Sat, 3 Oct 2009 19:06:05 -0400 Subject: [BiO BB] gff to sequence In-Reply-To: <55D5E770D835674587C89EE6239C5DAE1D4FFF4518@EXMBX06.ad.oak.ox.ac.uk> References: Message-ID: <55D5E770D835674587C89EE6239C5DAE1D4FFF4518 at EXMBX06.ad.oak.ox.ac.uk> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 > This seems of such general use that it begs a small utility which will > take a (possibly indexed) fasta file=2C a gff and output the sequences yo= u > want. What would people want from such a programme? > Is GTF (http://mblab.wustl.edu/GTF2.html) more useful or GFF? > Would different elements from the same group (gene/transcript) be joined > together in order? I wrote a small system like this based on ASCII hit files- this means most of your temp files can be processed with standard tools and usually they don't limit the speed although with cygwin going through windoze this can add up.=20 > Would one want filtering on the "features" column so one could retrieve a= ll > splice sites or codon exons? > What would be the output? Another fasta file? How would each "group" of > Sequences (e.g. transcript) be labelled? By a user supplied regular expre= ssion? > > >> I guess it depends what you mean by quick- quick to write you could use = awk >> but then it depends what additional things you want to do with results.= =3D20 >> I ended up writing a C++ fasta utility program since PERL can slow down = som=3D >> etimes but I ended up grabbing a couple of regex libraries to let me=3D2= 0 >> grep names etc.=3D20 > I hoped you used boost:regex which will be in the next c++ standard If you had to read my posts on their mail list youwould change your attitud= e=20 and wish I never heard of it:) Actually=2C as pointed out there=2C it isn't clear how fast it is compared to greta ( for all my complaints on msft that works well but maddock is at boost in any case). Finally I wrote my own limited compiler but there seem to be boost expression compilers that may be useful too. For editing fasta files=2C I doubt you care this much about regex speed however.=20 Note: hotmail is now unusable for TEXT=2C I am moving to marchywka at gmail.co= m or also use marchywka at yahoo.com. Thanks. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 415-264-8477 (w)<- use this 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff=2C I normally use for hobby/non-profit information but may use in investment forums=2C public and private. Please indicate any concerns if applicable. =0A= _________________________________________________________________=0A= Hotmail: Powerful Free email with security by Microsoft.=0A= http://clk.atdmt.com/GBL/go/171222986/direct/01/= From dan.bolser at gmail.com Mon Oct 5 04:22:33 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 5 Oct 2009 09:22:33 +0100 Subject: [BiO BB] gff to sequence In-Reply-To: <55D5E770D835674587C89EE6239C5DAE1D4FFF4518@EXMBX06.ad.oak.ox.ac.uk> References: <55D5E770D835674587C89EE6239C5DAE1D4FFF4518@EXMBX06.ad.oak.ox.ac.uk> Message-ID: <2c8757af0910050122v57296143p4abc2f6028e9727a@mail.gmail.com> 2009/10/3 Leo Goodstadt : >> >> Is there a way to quickly extract out the coordinates from a gff file >> >> and the corresponding sequence from a fasta file? >> >> >> > This seems of such general use that it begs a small utility which will > take a (possibly indexed) fasta file, a gff and output the sequences you > want. What would people want from such a programme? At least one user wants the following: given a GFF file, produce a multi Fasta sequence file with one sequence from each 'feature' in the GFF file. Each feature sequence should be derived from the corresponding reference sequence. Features should probably be restricted to certain types, as zero length or single base features are probably not that interesting. > Is GTF (http://mblab.wustl.edu/GTF2.html) more useful or GFF? > Would different elements from the same group (gene/transcript) be joined > together in order? I don't think so. I think GTF was invented to overcome some limitations with GFF2. However, GFF3 is now the standard: http://www.sequenceontology.org/gff3.shtml (I can't believe how incredibly annoying the background image for that page is!) As far as I know there are no pending 'improvements' to GFF3. > Would one want filtering on the "features" column so one could retrieve all > splice sites or codon exons? That would be a nice feature, and would be easy to implement. > What would be the output? Another fasta file? How would each "group" of > Sequences (e.g. transcript) be labelled? By a user supplied regular expression? I think the required output is a multi Fasta file. The GFF3 format requires each feature to have a unique ID, so I'd suggest simply using that as the sequence ID (no point re-inventing the wheel). You could then include the feature name (if present) and the reference sequence id in the remainder of the Fasta def line (http://en.wikipedia.org/wiki/FASTA_format). >> I guess it depends what you mean by quick- quick to write you could use awk >> but then it depends what additional things you want to do with results.=20 >> I ended up writing a C++ fasta utility program since PERL can slow down som= >> etimes but I ended up grabbing a couple of regex libraries to let me=20 >> grep names etc.=20 > I hoped you used boost:regex which will be in the next c++ standard > (http://www.boost.org/doc/libs/1_40_0/libs/regex/doc/html/index.html) and > is as easy to use and powerful as perl/python regular expressions (though > c rules on escaping backslashes are a pain). > Leo > Leo Goodstadt One thing to consider: if the reference sequence isn't part of the GFF file and/or isn't passed as a separate Fasta file, the DAS registry could be queried in order to obtain the URI of a reference server that provides the sequence: http://www.dasregistry.org/ That takes the project one step beyond a simple parser, so its something to think about rather than an explicit requirement. Otherwise I think your right, A little tool to do what you suggested could be very useful! Cheers, Dan. > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From pmr at ebi.ac.uk Tue Oct 6 07:07:37 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 06 Oct 2009 12:07:37 +0100 Subject: [BiO BB] gff to sequence In-Reply-To: References: Message-ID: <4ACB24F9.70509@ebi.ac.uk> On 03/10/09 01:29, Kie Kyon Huang wrote: > Hi, > > Is there a way to quickly extract out the coordinates from a gff file > and the corresponding sequence from a fasta file? EMBOSS can do this. Sequences can be read from FASTA and feature tables from GFF (gff2 or gff3) extractfeat seqfile.fasta -ufo featfile.gff -out features.fasta The output file (features.fasta) will have the sequences of all the features with the positions and the feature type, for example: >X13776_8_24 [promoter] Pseudomonas aeruginosa amiC and amiR gene ctggccgagcatctgct >X13776_65_81 [promoter] Pseudomonas aeruginosa amiC and amiR gene ctggcgagcctggagca >X13776_121_126 [RBS] Pseudomonas aeruginosa amiC and amiR gene aggaga Hope this helps Peter Rice From danielucg at yahoo.com.br Tue Oct 6 09:32:24 2009 From: danielucg at yahoo.com.br (Daniel Xavier de Sousa) Date: Tue, 6 Oct 2009 06:32:24 -0700 (PDT) Subject: [BiO BB] Pipeline Tool Message-ID: <258279.4749.qm@web52406.mail.re2.yahoo.com> Hi Everybody, I'm looking for a tool for run Genome Project. In other words, I want a system web to submit chromatogram, and process on it bases calling (PHRED), vector cleaning (CROSS_MATCH), clustering (CAP3) and annotation (BLAST) - PIPELINE. And I would like to see all data on graphic interface. I have tried many others tools, as ESTWeb. But all them have different problems: the project has finished, there is not support, there is no lab using,... I have searched Google, Bioinformatics.ORG, ... But,I`m asking here because I would like to get some one that there are labs using it. No matter if the tool is comercial (have to pay for it). I really want resolve my problem of pipeline process. Can anyone, suggest one? Thanks, -Daniel Xavier de Sousa ________________________________ Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - M?sica - Esportes ____________________________________________________________________________________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com From harry.mangalam at uci.edu Tue Oct 6 16:28:33 2009 From: harry.mangalam at uci.edu (Harry Mangalam) Date: Tue, 6 Oct 2009 13:28:33 -0700 Subject: [BiO BB] Pipeline Tool In-Reply-To: <258279.4749.qm@web52406.mail.re2.yahoo.com> References: <258279.4749.qm@web52406.mail.re2.yahoo.com> Message-ID: <200910061328.33287.harry.mangalam@uci.edu> There's a very expensive commercial tool called Scitegic's Pipeline Pilot (may be been re-ingested by Accelerys). It's very well-designed (and should be for the price), but it runs only on MS Windows (tho some back end stuff may now run on *nix). However, you could do a lot worse than try VisTrails. A supported Open Source PyQt-based visual workflow, it's meant to be easy to install (especially on Linux) and very easy to use & debug. It's an ongoing project and the developers are very responsive and have one of the best senses of how to implement a UI of the OSS ones I've seen/used. It also tracks the changes of the workflow in a very subversion-like way (the 'trails' part of it). It balances ease of use with power in ways that others have not seen fit to do (see Kepler - enormously powerful, unusably complicated IMHO..) http://www.vistrails.org/index.php/Main_Page hjm On Tuesday 06 October 2009 06:32:24 Daniel Xavier de Sousa wrote: > Hi Everybody, > > > I'm looking for a tool for run Genome Project. In other words, I want a > system web to submit chromatogram, and process on it bases calling (PHRED), > vector cleaning (CROSS_MATCH), clustering (CAP3) and annotation (BLAST) - > PIPELINE. And I would like to see all data on graphic interface. > > I have tried many others tools, as ESTWeb. But all them have different > problems: the project has finished, there is not support, there is no lab > using,... > > I have searched Google, Bioinformatics.ORG, ... But,I`m asking here because > I would like to get some one that there are labs using it. > > No matter if the tool is comercial (have to pay for it). I really want > resolve my problem of pipeline process. > > > > Can anyone, suggest one? > > > Thanks, > -Daniel Xavier de Sousa > ________________________________ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - > Celebridades - M?sica - Esportes > > > > ___________________________________________________________________________ >_________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados > http://br.maisbuscados.yahoo.com > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb -- Harry Mangalam - Research Computing, NACS, Rm 225 MSTB, UC Irvine [ZOT 2225] / 92697 949 824-0084(o), 949 285-4487(c) MSTB=Bldg 415 (G-5 on --- It is better to be roughly right than precisely wrong. Keynes From golharam at umdnj.edu Tue Oct 6 16:47:08 2009 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 06 Oct 2009 16:47:08 -0400 Subject: [BiO BB] Pipeline Tool In-Reply-To: <200910061328.33287.harry.mangalam@uci.edu> References: <258279.4749.qm@web52406.mail.re2.yahoo.com> <200910061328.33287.harry.mangalam@uci.edu> Message-ID: <4ACBACCC.20209@umdnj.edu> I create a program to do exactly this back in 2001 using Java. Its a nice interface and worked well. I wonder if I can upload it somewhere for public use. Perhaps on bioinformatics.org? Harry Mangalam wrote: > There's a very expensive commercial tool called Scitegic's Pipeline Pilot (may > be been re-ingested by Accelerys). It's very well-designed (and should be > for the price), but it runs only on MS Windows (tho some back end stuff may > now run on *nix). > > However, you could do a lot worse than try VisTrails. A supported Open Source > PyQt-based visual workflow, it's meant to be easy to install (especially on > Linux) and very easy to use & debug. It's an ongoing project and the > developers are very responsive and have one of the best senses of how to > implement a UI of the OSS ones I've seen/used. It also tracks the changes of > the workflow in a very subversion-like way (the 'trails' part of it). It > balances ease of use with power in ways that others have not seen fit to do > (see Kepler - enormously powerful, unusably complicated IMHO..) > > http://www.vistrails.org/index.php/Main_Page > > hjm > > On Tuesday 06 October 2009 06:32:24 Daniel Xavier de Sousa wrote: >> Hi Everybody, >> >> >> I'm looking for a tool for run Genome Project. In other words, I want a >> system web to submit chromatogram, and process on it bases calling (PHRED), >> vector cleaning (CROSS_MATCH), clustering (CAP3) and annotation (BLAST) - >> PIPELINE. And I would like to see all data on graphic interface. >> >> I have tried many others tools, as ESTWeb. But all them have different >> problems: the project has finished, there is not support, there is no lab >> using,... >> >> I have searched Google, Bioinformatics.ORG, ... But,I`m asking here because >> I would like to get some one that there are labs using it. >> >> No matter if the tool is comercial (have to pay for it). I really want >> resolve my problem of pipeline process. >> >> >> >> Can anyone, suggest one? >> >> >> Thanks, >> -Daniel Xavier de Sousa >> ________________________________ >> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - >> Celebridades - M?sica - Esportes >> >> >> >> ___________________________________________________________________________ >> _________ Veja quais s?o os assuntos do momento no Yahoo! +Buscados >> http://br.maisbuscados.yahoo.com >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb > > > From jeff at bioinformatics.org Tue Oct 6 17:00:12 2009 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 06 Oct 2009 17:00:12 -0400 Subject: [BiO BB] Pipeline Tool In-Reply-To: <4ACBACCC.20209@umdnj.edu> References: <258279.4749.qm@web52406.mail.re2.yahoo.com> <200910061328.33287.harry.mangalam@uci.edu> <4ACBACCC.20209@umdnj.edu> Message-ID: <4ACBAFDC.6000001@bioinformatics.org> Hi Ryan, You're certainly welcome to create a new group at Bioinformatics.Org and upload your open-source licensed software (http://opensource.org/licenses/). Just log into the website, and you can register your group: http://www.bioinformatics.org/register/ Cheers, Jeff Ryan Golhar wrote: > I create a program to do exactly this back in 2001 using Java. Its a > nice interface and worked well. I wonder if I can upload it somewhere > for public use. Perhaps on bioinformatics.org? -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 978 621 8258 -- From marty.gollery at gmail.com Tue Oct 6 17:20:58 2009 From: marty.gollery at gmail.com (Martin Gollery) Date: Tue, 6 Oct 2009 14:20:58 -0700 Subject: [BiO BB] Pipeline Tool In-Reply-To: <258279.4749.qm@web52406.mail.re2.yahoo.com> References: <258279.4749.qm@web52406.mail.re2.yahoo.com> Message-ID: Hi Daniel, There are commercial packages to build things like this- Pipeline Pilot, ACGTuate and VIBE come to mind. Free tools include Taverna, BIP and BioGent. It sounds, however, like you want something premade. Take a look at Trace2dbEST, as this may do the trick. It is part of the BioLinux project, which can easily be installed and has many other modules as well. Best, Marty On Tue, Oct 6, 2009 at 6:32 AM, Daniel Xavier de Sousa < danielucg at yahoo.com.br> wrote: > Hi Everybody, > > > I'm looking for a tool for run Genome Project. In other words, I want a > system web to submit chromatogram, and process on it bases calling (PHRED), > vector cleaning (CROSS_MATCH), clustering (CAP3) and annotation (BLAST) - > PIPELINE. And I would like to see all data on graphic interface. > > I have tried many others tools, as ESTWeb. But all them have different > problems: the project has finished, there is not support, there is no lab > using,... > > I have searched Google, Bioinformatics.ORG, ... But,I`m asking here because > I would like to get some one that there are labs using it. > > No matter if the tool is comercial (have to pay for it). I really want > resolve my problem of pipeline process. > > > > Can anyone, suggest one? > > > Thanks, > -Daniel Xavier de Sousa > ________________________________ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - > Celebridades - M?sica - Esportes > > > > ____________________________________________________________________________________ > Veja quais s?o os assuntos do momento no Yahoo! +Buscados > http://br.maisbuscados.yahoo.com > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- -- Martin Gollery Senior Bioinformatics Scientist Tahoe Informatics www.bioinformaticist.biz www.hiddenmarkovmodels.com From prohan at gmail.com Tue Oct 6 21:34:23 2009 From: prohan at gmail.com (Rohan Sachdeva) Date: Tue, 6 Oct 2009 18:34:23 -0700 Subject: [BiO BB] Pipeline Tool In-Reply-To: <258279.4749.qm@web52406.mail.re2.yahoo.com> References: <258279.4749.qm@web52406.mail.re2.yahoo.com> Message-ID: <797845434991089156@unknownmsgid> The program geneious does all of this... I'm not too sure about it's annotation features though. On Oct 6, 2009, at 12:57 PM, Daniel Xavier de Sousa wrote: > Hi Everybody, > > > I'm looking for a tool for run Genome Project. In other words, I > want a system web to submit chromatogram, and process on it bases > calling (PHRED), vector cleaning (CROSS_MATCH), clustering (CAP3) > and annotation (BLAST) - PIPELINE. And I would like to see all data > on graphic interface. > > I have tried many others tools, as ESTWeb. But all them have > different problems: the project has finished, there is not support, > there is no lab using,... > > I have searched Google, Bioinformatics.ORG, ... But,I`m asking here > because I would like to get some one that there are labs using it. > > No matter if the tool is comercial (have to pay for it). I really > want resolve my problem of pipeline process. > > > > Can anyone, suggest one? > > > Thanks, > -Daniel Xavier de Sousa > ________________________________ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - > Celebridades - M?sica - Esportes > > > > ____________________________________________________________________________________ > Veja quais s?o os assuntos do momento no Yahoo! +Buscados > http://br.maisbuscados.yahoo.com > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb From jforment at ibmcp.upv.es Wed Oct 7 03:28:06 2009 From: jforment at ibmcp.upv.es (Javier Forment Millet) Date: Wed, 7 Oct 2009 09:28:06 +0200 Subject: [BiO BB] Pipeline Tool In-Reply-To: <258279.4749.qm@web52406.mail.re2.yahoo.com> References: <258279.4749.qm@web52406.mail.re2.yahoo.com> Message-ID: <1254900486.4acc43068f4a2@webmail.upv.es> Hi, We developed an open-source EST analysis tool for our respective EST projects which runs automatically from the chromatogram files to the population of a database with a web graphical front-end and strong capabilities of data mining. See the paper (BMC Bioinformatics 2008, 9:5) at http://www.biomedcentral.com/1471-2105/9/5). You can freely download it from http://bioinf.comav.upv.es/est2uni/ We are using from 2005 and there is a user's community which continues improving the tool from a distribution list (https://listas.upv.es/mailman/listinfo/est2uni). Hope it helps, Javier. Quoting Daniel Xavier de Sousa : > Hi Everybody, > > > I'm looking for a tool for run Genome Project. In other words, I want a > system web to submit chromatogram, and process on it bases calling (PHRED), > vector cleaning (CROSS_MATCH), clustering (CAP3) and annotation (BLAST) - > PIPELINE. And I would like to see all data on graphic interface. > > I have tried many others tools, as ESTWeb. But all them have different > problems: the project has finished, there is not support, there is no lab > using,... > > I have searched Google, Bioinformatics.ORG, ... But,I`m asking here because I > would like to get some one that there are labs using it. > > No matter if the tool is comercial (have to pay for it). I really want > resolve my problem of pipeline process. > > > > Can anyone, suggest one? > > > Thanks, > -Daniel Xavier de Sousa > ________________________________ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - > Celebridades - M?sica - Esportes > > > > ____________________________________________________________________________________ > Veja quais s?o os assuntos do momento no Yahoo! +Buscados > http://br.maisbuscados.yahoo.com > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Javier Forment Millet Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta E Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain Tlf.:+34-96-3877858 (ext. 77858) FAX: +34-96-3877859 jforment at ibmcp.upv.es From golharam at umdnj.edu Wed Oct 7 23:06:49 2009 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 07 Oct 2009 23:06:49 -0400 Subject: [BiO BB] Pipeline Tool In-Reply-To: <797845434991089156@unknownmsgid> References: <258279.4749.qm@web52406.mail.re2.yahoo.com> <797845434991089156@unknownmsgid> Message-ID: <4ACD5749.6030104@umdnj.edu> Can you plug in modules into Genious? Its got a nice interface, but its not open-source, and there is a lot I'd love to add to it. Rohan Sachdeva wrote: > The program geneious does all of this... I'm not too sure about it's > annotation features though. > > On Oct 6, 2009, at 12:57 PM, Daniel Xavier de Sousa > wrote: > >> Hi Everybody, >> >> >> I'm looking for a tool for run Genome Project. In other words, I >> want a system web to submit chromatogram, and process on it bases >> calling (PHRED), vector cleaning (CROSS_MATCH), clustering (CAP3) >> and annotation (BLAST) - PIPELINE. And I would like to see all data >> on graphic interface. >> >> I have tried many others tools, as ESTWeb. But all them have >> different problems: the project has finished, there is not support, >> there is no lab using,... >> >> I have searched Google, Bioinformatics.ORG, ... But,I`m asking here >> because I would like to get some one that there are labs using it. >> >> No matter if the tool is comercial (have to pay for it). I really >> want resolve my problem of pipeline process. >> >> >> >> Can anyone, suggest one? >> >> >> Thanks, >> -Daniel Xavier de Sousa >> ________________________________ >> Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - >> Celebridades - M?sica - Esportes >> >> >> >> ____________________________________________________________________________________ > > >> Veja quais s?o os assuntos do momento no Yahoo! +Buscados >> http://br.maisbuscados.yahoo.com >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From events at embl-events.de Wed Oct 21 09:00:12 2009 From: events at embl-events.de (EMBL Courses & Conferences) Date: Wed, 21 Oct 2009 15:00:12 +0200 Subject: [BiO BB] Visualizing Biological Data, 3-5 March 2010: Deadline on 16 Nov 2009 Message-ID: <0LrG8W-1MFXVz3K72-01360m@mrelayeu.kundenserver.de> Dear colleagues, We invite you to participate in the first EMBO Workshop on Visualizing Biological Data (VizBi, http://www.vizbi.org) 3 - 5 March 2010 at the EMBL's new Advanced Training Centre in Heidelberg, Germany The goal of the workshop is to bring together, for the first time, researchers developing and using visualization systems across all areas of biology, including genomics, sequence analysis, macromolecular structures, systems biology, and imaging (including microscopy and magnetic resonance imaging). We have assembled an authoritative list of 29 invited speakers who will present an exciting program, reviewing the state-of-the-art and perspectives in each of these areas. The primary focus will be on visualizing processed and annotated data in their biological context, rather than on processing of raw data. The workshop is limited in the total number participants, and each participant is normally required to present a poster and to give a 'fastforward' presentation about their work (limited to 30 seconds and 1 slide). To apply to join the workshop, please go to http://vizbi.org and submit an abstract and image related to your work. Submissions close on 16 November 2009. Since places are limited, participants will be selected based on the relevance of their work to the goals of the workshop. Notifications of acceptance will be sent within three weeks after the close of submissions. We plan to award a prize for the submitted image that best conveys a strong scientific message in a visually compelling manner. Please forward this announcement to anyone who may be interested. We hope to see you in Heidelberg next spring! Se??n O'Donoghue, EMBL Jim Procter, University of Dundee Nils Gehlenborg, European Bioinformatics Institute Reinhard Schneider, EMBL If you have any questions about the registration process please contact: Adela Valceanu Conference Officer European Molecular Biology Laboratory Meyerhofstr. 1 D-69117 Heidelberg Tel: +49-6221-387 8625 Fax: +49-6221-387 8158 Email: valceanu at embl.de For full event listings please visit our website: www.embl.org/events or sign up for our newsletter www.embl.de/events/newsletter From avinash.abhyankar at gmail.com Thu Oct 22 04:30:52 2009 From: avinash.abhyankar at gmail.com (Avinash Abhyankar) Date: Thu, 22 Oct 2009 10:30:52 +0200 Subject: [BiO BB] next-gen sequencing workshops? Message-ID: Dear friends, Does anyone know of workshops or similar events that will impart training in analysis of next-gen sequencing data especially related to SNP discovery. I am looking for such events to be held between November 2009 to February 2010. Thanks in advance. Avinash __________________________________ Avinash Abhyankar Medical Genetics Unit Department of Clinical Sciences, Malm? Clinical Research Center Entrance 72, Bldg 91, Floor 11 University Hospital MAS, 205 02 Malm? Office: (040)391160 Mobile: 0735010538 From dan.bolser at gmail.com Fri Oct 23 04:03:14 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Fri, 23 Oct 2009 09:03:14 +0100 Subject: [BiO BB] next-gen sequencing workshops? In-Reply-To: References: Message-ID: <2c8757af0910230103l609513e7le23beade051b7c96@mail.gmail.com> Try asking on http://SEQanswers.com 2009/10/22 Avinash Abhyankar : > Dear friends, > Does anyone know of workshops or similar events that will impart training in > analysis of next-gen sequencing data especially related to SNP discovery. I > am looking for such events to be held between November 2009 to February > 2010. > Thanks in advance. > Avinash > __________________________________ > Avinash Abhyankar > Medical Genetics Unit > Department of Clinical Sciences, Malm? > Clinical Research Center > Entrance 72, Bldg 91, Floor 11 > University Hospital MAS, 205 02 Malm? > Office: (040)391160 > Mobile: 0735010538 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From pfern at igc.gulbenkian.pt Fri Oct 23 04:57:43 2009 From: pfern at igc.gulbenkian.pt (Pedro Fernandes) Date: Fri, 23 Oct 2009 09:57:43 +0100 Subject: [BiO BB] next-gen sequencing workshops? In-Reply-To: <2c8757af0910230103l609513e7le23beade051b7c96@mail.gmail.com> References: <2c8757af0910230103l609513e7le23beade051b7c96@mail.gmail.com> Message-ID: <1256288263.4ae170070b748@webmail.igc.gulbenkian.pt> You may still register in our conference http://www.bioinformatics-portugal.org/jb2009 JB2009 -- Pedro Fernandes Chair, JB2009 Centro Portugu?s de Bioinform?tica Instituto Gulbenkian de Ci?ncia Apartado 14 2781 OEIRAS PORTUGAL Quoting Dan Bolser : > Try asking on http://SEQanswers.com > > 2009/10/22 Avinash Abhyankar : > > Dear friends, > > Does anyone know of workshops or similar events that will impart training > in > > analysis of next-gen sequencing data especially related to SNP discovery. I > > am looking for such events to be held between November 2009 to February > > 2010. > > Thanks in advance. > > Avinash > > __________________________________ > > Avinash Abhyankar > > Medical Genetics Unit > > Department of Clinical Sciences, Malm? > > Clinical Research Center > > Entrance 72, Bldg 91, Floor 11 > > University Hospital MAS, 205 02 Malm? > > Office: (040)391160 > > Mobile: 0735010538 > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb >