From barry.hardy at vtxmail.ch Tue May 6 14:02:39 2008 From: barry.hardy at vtxmail.ch (Barry Hardy) Date: Tue, 06 May 2008 20:02:39 +0200 Subject: [BiO BB] Program for eCheminfo Drug Discovery Workshop Week (Oxford, 21-25 July 2008) Message-ID: <48209D3F.70609@vtxmail.ch> The program, abstracts and schedule for the 5 Day eCheminfo Hands-on Drug Discovery Workshop Week (21-25 July 2008) at the Medical Sciences Teaching Center, Oxford University, Oxford, UK is now available at: http://barryhardy.blogs.com/cheminfostream/2008/05/program-schedul.html Topics to be covered: Virtual Screening & Docking; Structure-based Drug Design; Ligand Optimisation & Library Design; Structure Search, Similarity and Property Estimation; Data Mining, Analysis & Visualisation; Pharmacophore Modelling for Lead Identification; Fragment-based Drug Design; QSAR-based Predictive Toxicology; and Quantitative Spectrometric Data-Activity Relationship Modelling. To complete registration arrangements for the workshop, please contact Nicki.Douglas ?(at)- douglasconnect.com, +41 61 851 0461 best regards Barry Hardy eCheminfo Community of Practice http://echeminfo.colayer.net/ Douglas Connect +41 61 851 0170 From me.lixue at gmail.com Tue May 27 11:05:02 2008 From: me.lixue at gmail.com (Xue Li) Date: Tue, 27 May 2008 10:05:02 -0500 Subject: [BiO BB] how pdb ID is defined? In-Reply-To: <62ed16460805241813o285a9468u5b5815088f74bbb2@mail.gmail.com> References: <62ed16460805241813o285a9468u5b5815088f74bbb2@mail.gmail.com> Message-ID: <62ed16460805270805n6ba6b310g3bfba4966b6256e5@mail.gmail.com> Dear all, Maybe this is a naive question. I just noticed that proteins 2GSA and 4GSA have similar name and denote almost the same protein. 4gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE (AMINOTRANSFERASE) REDUCED WITH CYANOBOROHYDRATE 2gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE (AMINOTRANSFERASE, WILD-TYPE FORM) Also, 2ae2 and 1ae1 denote similar proteins. 2ae2: TROPINONE REDUCTASE-II COMPLEXED WITH NADP+ AND PSEUDOTROPINE 1ae1: TROPINONE REDUCTASE-I COMPLEX WITH NADP Would someone please tell me how PDB ID is defined? Given a list of pdb ID, can I find biological distance merely based on their pdb IDs? Thanks a lot. -- Xue, Li Bioinformatics and Computational Biology program @ ISU Ames, IA 50010 515-450-7183 From hiekeen at gmail.com Tue May 27 11:58:55 2008 From: hiekeen at gmail.com (Jinyan Huang) Date: Tue, 27 May 2008 23:58:55 +0800 Subject: [BiO BB] How to get the special Transcription Factor target sequences? Message-ID: I want to get the Transcription Factor target sequences. They are Oct4?Sox2?cMyc?Klf4?Nanog?Lin28. Is there such free database? Or should I just search it one by one from the literature? -- Best regards, Jinyan Huang (ekeen) School of Life Sciences and Technology, 1302 Room Tongji University Siping Road 1239, Shanghai 200092 P.R. China Tel :0086-21-65981041 Msn: hiekeen at hotmail.com eMail: hiekeen at gmail.com From jgbaum at gmail.com Tue May 27 13:03:19 2008 From: jgbaum at gmail.com (J Greenbaum) Date: Tue, 27 May 2008 10:03:19 -0700 Subject: [BiO BB] How to get the special Transcription Factor target sequences? In-Reply-To: References: Message-ID: <701a2c50805271003r2dd3945cv67f3f28d1b10ef54@mail.gmail.com> The Transfac database (www.gene-regulation.com/pub/databases.html) should have what you are looking for... Jason Greenbaum Postdoctoral Fellow La Jolla Institute for Allergy & Immunology 2008/5/27 Jinyan Huang : > I want to get the Transcription Factor target sequences. They are > Oct4?Sox2?cMyc?Klf4?Nanog?Lin28. > Is there such free database? Or should I just search it one by one > from the literature? > > > -- > Best regards, > Jinyan Huang (ekeen) > School of Life Sciences and Technology, 1302 Room > Tongji University > Siping Road 1239, Shanghai 200092 > P.R. China > Tel :0086-21-65981041 > Msn: hiekeen at hotmail.com > eMail: hiekeen at gmail.com > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From silkhuang at gmail.com Tue May 27 21:56:18 2008 From: silkhuang at gmail.com (Huang Tao) Date: Wed, 28 May 2008 09:56:18 +0800 Subject: [BiO BB] how pdb ID is defined? In-Reply-To: <62ed16460805270805n6ba6b310g3bfba4966b6256e5@mail.gmail.com> References: <62ed16460805241813o285a9468u5b5815088f74bbb2@mail.gmail.com> <62ed16460805270805n6ba6b310g3bfba4966b6256e5@mail.gmail.com> Message-ID: <5db67c690805271856o7ece427ckbe0582b251b83bd@mail.gmail.com> About PDB ID, please refer to: http://www.rcsb.org/robohelp/search_database/pdb_identifier.htm. Usually, you will find the last three characters is an abbreviation of certain protein name. For example, there is an entry of ubiquitin of which PDB ID is 1UBQ. However, you should not determine *biological distance merely based on their pdb IDs*. It's possible, but not absolutely right. You may use sequence alignment tools (e.g. ClustalW) to determine the biological distance between your interested proteins, or use "Sequence Search (http://www.rcsb.org/pdb/search/searchSequence.do)" provided by RCSB PDB to find similar proteins, actually, it is a BLAST service. Cheers, Tao 2008/5/27 Xue Li : > Dear all, > > Maybe this is a naive question. I just noticed that proteins 2GSA and > 4GSA have similar name and denote almost the same protein. > > 4gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE > (AMINOTRANSFERASE) REDUCED WITH CYANOBOROHYDRATE > 2gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE > AMINOMUTASE (AMINOTRANSFERASE, WILD-TYPE FORM) > > Also, 2ae2 and 1ae1 denote similar proteins. > 2ae2: TROPINONE REDUCTASE-II COMPLEXED WITH NADP+ AND PSEUDOTROPINE > 1ae1: TROPINONE REDUCTASE-I COMPLEX WITH NADP > > > Would someone please tell me how PDB ID is defined? Given a list of > pdb ID, can I find biological distance merely based on their pdb IDs? > > Thanks a lot. > > -- > Xue, Li > Bioinformatics and Computational Biology program @ ISU > Ames, IA 50010 > 515-450-7183 > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- ??? Tao Huang From hiekeen at gmail.com Wed May 28 03:16:32 2008 From: hiekeen at gmail.com (Jinyan Huang) Date: Wed, 28 May 2008 15:16:32 +0800 Subject: [BiO BB] How to get the special Transcription Factor target sequences? In-Reply-To: <701a2c50805271003r2dd3945cv67f3f28d1b10ef54@mail.gmail.com> References: <701a2c50805271003r2dd3945cv67f3f28d1b10ef54@mail.gmail.com> Message-ID: It seems it is hard to pass the registration. 2008/5/28 J Greenbaum : > The Transfac database (www.gene-regulation.com/pub/databases.html) > should have what you are looking for... > > Jason Greenbaum > Postdoctoral Fellow > La Jolla Institute for Allergy & Immunology > > 2008/5/27 Jinyan Huang : >> I want to get the Transcription Factor target sequences. They are >> Oct4?Sox2?cMyc?Klf4?Nanog?Lin28. >> Is there such free database? Or should I just search it one by one >> from the literature? >> >> >> -- >> Best regards, >> Jinyan Huang (ekeen) >> School of Life Sciences and Technology, 1302 Room >> Tongji University >> Siping Road 1239, Shanghai 200092 >> P.R. China >> Tel :0086-21-65981041 >> Msn: hiekeen at hotmail.com >> eMail: hiekeen at gmail.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 > -- Best regards, Jinyan Huang (ekeen) School of Life Sciences and Technology, 1302 Room Tongji University Siping Road 1239, Shanghai 200092 P.R. China Tel :0086-21-65981041 Msn: hiekeen at hotmail.com eMail: hiekeen at gmail.com From marchywka at hotmail.com Wed May 28 12:54:14 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Wed, 28 May 2008 12:54:14 -0400 Subject: [BiO BB] how pdb ID is defined? In-Reply-To: <5db67c690805271856o7ece427ckbe0582b251b83bd@mail.gmail.com> References: <62ed16460805241813o285a9468u5b5815088f74bbb2@mail.gmail.com> <62ed16460805270805n6ba6b310g3bfba4966b6256e5@mail.gmail.com> <5db67c690805271856o7ece427ckbe0582b251b83bd@mail.gmail.com> Message-ID: > You may use sequence alignment tools (e.g. ClustalW) to determine the > biological distance between your interested proteins, or use "Sequence > Search (http://www.rcsb.org/pdb/search/searchSequence.do)" provided by RCSB > PDB to find similar proteins, actually, it is a BLAST service. I actually "discovered" the redundancy in the entries by accident trying to make a 3D lookup tool. So, I have a couple of comments. 1) Are there 3D lookup databases? I think this came up earlier but I'm not sure anyone completely answered although we discussed 3D alignment tools for given entries, I'm not sure you could make a 3D query. 2) I've gotten a ( non-useful ) tool to work on a "database" of a few hundred pdb files. In fact, the tool could accept a query and find exact 3D matches ( rotationally invariant ) but it was awful at finding "similar" things- I got lots of hits but noted all the names were similar as per the earlier comments. I stopped at this point and went back to various topics like mechanical CAD literature to see if I could improve the approach. I have some examples posted here ( and you will note that I have placeholder/failures up there right now but don't intend to fix right away): http://www.spottext.com/marchywka/glutp/docs_surfaces.html?src=biolist If anyone has links to papers on surface descption algorithms they may be helpful in refining the approach. The surface FINDER looks ok as it seems to separate solvent accessible patches from those hidden ( and presumably less relevant ) but I can't quite make a database that can be reasonably queried for biologically similar components ( like cavities for example). Thanks. > Date: Wed, 28 May 2008 09:56:18 +0800 > From: silkhuang at gmail.com > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] how pdb ID is defined? > > _________________________________________________________________ Give to a good cause with every e-mail. Join the i?m Initiative from Microsoft. http://im.live.com/Messenger/IM/Join/Default.aspx?souce=EML_WL_ GoodCause From me.lixue at gmail.com Wed May 28 12:44:16 2008 From: me.lixue at gmail.com (Xue Li) Date: Wed, 28 May 2008 11:44:16 -0500 Subject: [BiO BB] how pdb ID is defined? In-Reply-To: <5db67c690805271856o7ece427ckbe0582b251b83bd@mail.gmail.com> References: <62ed16460805241813o285a9468u5b5815088f74bbb2@mail.gmail.com> <62ed16460805270805n6ba6b310g3bfba4966b6256e5@mail.gmail.com> <5db67c690805271856o7ece427ckbe0582b251b83bd@mail.gmail.com> Message-ID: <62ed16460805280944we37be43q8b980b05b81f12b6@mail.gmail.com> Hi Tao, Thank you very much for your reply. Yes, you are right. I also find the following link saying: 3 Policy regarding assignment of PDB IDs Can a PDB ID be requested? Neither a single PDB IDs nor a range of PDB IDs can be requested. PDB ID codes are automatically assigned and do not have any meaning. When are PDB IDs assigned? PDB IDs are automatically assigned by software when the author has completed his/her deposition (i.e. the author has filled out at least the minimal information for deposition and has pressed the deposit & confirmation buttons.) http://www.wwpdb.org/documentation/wwPDB-B-20070529.pdf page 9 Thank you, Li 2008/5/27 Huang Tao : > About PDB ID, please refer to: > http://www.rcsb.org/robohelp/search_database/pdb_identifier.htm. > > Usually, you will find the last three characters is an abbreviation of > certain protein name. For example, there is an entry of ubiquitin of which > PDB ID is 1UBQ. However, you should not determine *biological distance > merely based on their pdb IDs*. It's possible, but not absolutely right. > > You may use sequence alignment tools (e.g. ClustalW) to determine the > biological distance between your interested proteins, or use "Sequence > Search (http://www.rcsb.org/pdb/search/searchSequence.do)" provided by RCSB > PDB to find similar proteins, actually, it is a BLAST service. > > > Cheers, > > Tao > > 2008/5/27 Xue Li : > >> Dear all, >> >> Maybe this is a naive question. I just noticed that proteins 2GSA and >> 4GSA have similar name and denote almost the same protein. >> >> 4gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE >> (AMINOTRANSFERASE) REDUCED WITH CYANOBOROHYDRATE >> 2gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE >> AMINOMUTASE (AMINOTRANSFERASE, WILD-TYPE FORM) >> >> Also, 2ae2 and 1ae1 denote similar proteins. >> 2ae2: TROPINONE REDUCTASE-II COMPLEXED WITH NADP+ AND PSEUDOTROPINE >> 1ae1: TROPINONE REDUCTASE-I COMPLEX WITH NADP >> >> >> Would someone please tell me how PDB ID is defined? Given a list of >> pdb ID, can I find biological distance merely based on their pdb IDs? >> >> Thanks a lot. >> >> -- >> Xue, Li >> Bioinformatics and Computational Biology program @ ISU >> Ames, IA 50010 >> 515-450-7183 >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > > > -- > ??? Tao Huang > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Xue, Li Bioinformatics and Computational Biology program @ ISU Ames, IA 50010 515-450-7183 From lichunjiang at sibs.ac.cn Wed May 28 13:35:27 2008 From: lichunjiang at sibs.ac.cn (lichunjiang) Date: Thu, 29 May 2008 01:35:27 +0800 (CST) Subject: [BiO BB] How to get the special Transcription Factor target sequences? In-Reply-To: References: <701a2c50805271003r2dd3945cv67f3f28d1b10ef54@mail.gmail.com> Message-ID: <3400.66.44.122.59.1211996127.squirrel@webmail.sibs.ac.cn> Really? I registrated for gene-regulation.com a couple of years ago, it is quite easy.? It does not make sense that you can not register. Or you should just write to the service to fix the problem. Actually, it is free to use a reduced version. For the full professional version, you need to pay. Besides Transfac, I recommend another database: JARSPAR available at http://jaspar.genereg.net/.? It is totally free to use. Hope this help. Good luck! > It seems it is hard to pass the registration. > > 2008/5/28 J Greenbaum : >> The Transfac database (www.gene-regulation.com/pub/databases.html) >> should have what you are looking for... >> >> Jason Greenbaum >> Postdoctoral Fellow >> La Jolla Institute for Allergy & Immunology >> >> 2008/5/27 Jinyan Huang : >>> I want to get the Transcription Factor target sequences. They are >>> Oct4,Sox2,cMyc,Klf4,Nanog,Lin28. >>> Is there such free database? Or should I just search it one by one >>> from the literature? >>> >>> >>> -- >>> Best regards, >>> Jinyan Huang (ekeen) >>> School of Life Sciences and Technology, 1302 Room >>> Tongji University >>> Siping Road 1239, Shanghai 200092 >>> P.R. China >>> Tel :0086-21-65981041 >>> Msn: hiekeen at hotmail.com >>> eMail: hiekeen at gmail.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 >> > > > > -- > Best regards, > Jinyan Huang (ekeen) > School of Life Sciences and Technology, 1302 Room > Tongji University > Siping Road 1239, Shanghai 200092 > P.R. China > Tel :0086-21-65981041 > Msn: hiekeen at hotmail.com > eMail: hiekeen at gmail.com > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > -- lichunjiang at sibs.ac.cn Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences From me.lixue at gmail.com Wed May 28 14:37:38 2008 From: me.lixue at gmail.com (Xue Li) Date: Wed, 28 May 2008 13:37:38 -0500 Subject: [BiO BB] may I use GO to identify functional similar proteins Message-ID: <62ed16460805281137k57acbb29h75f7f1d86548c8f9@mail.gmail.com> Hello all, Does anyone know whether I could use GO to identify functional similar proteins? Given a protein pdbID, can I search GO for functional similar proteins? Thanks. -- Xue, Li Bioinformatics and Computational Biology program @ ISU Ames, IA 50010 515-450-7183 From boris.steipe at utoronto.ca Wed May 28 15:32:59 2008 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Wed, 28 May 2008 15:32:59 -0400 Subject: [BiO BB] may I use GO to identify functional similar proteins In-Reply-To: <62ed16460805281137k57acbb29h75f7f1d86548c8f9@mail.gmail.com> References: <62ed16460805281137k57acbb29h75f7f1d86548c8f9@mail.gmail.com> Message-ID: A number of similarity measures on GO have been defined in the literature. Once you have a PDB ID, get the corresponding UniProt ID, then use FunSimMat to find other proteins of similar function. The authors discuss the concepts and pitfalls of such an approach in their 2007 NAR paper. http://funsimmat.bioinf.mpi-inf.mpg.de/ However this approach does not really operate on independent data: a very large number of GO annotations is "inferred from electronic annotation" - i.e. more or less from a BLAST search. You are likely to get very similar information by simply doing a BLAST (or VAST) search in the first place: homologous proteins have similar function. But try it, it's quite informative. HTH, Boris On 28-May-08, at 2:37 PM, Xue Li wrote: > Hello all, > > Does anyone know whether I could use GO to identify functional similar > proteins? Given a protein pdbID, can I search GO for functional > similar proteins? Thanks. > > -- > Xue, Li > Bioinformatics and Computational Biology program @ ISU > Ames, IA 50010 > 515-450-7183 > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb From cjm at fruitfly.org Wed May 28 17:21:42 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Wed, 28 May 2008 14:21:42 -0700 Subject: [BiO BB] may I use GO to identify functional similar proteins In-Reply-To: References: <62ed16460805281137k57acbb29h75f7f1d86548c8f9@mail.gmail.com> Message-ID: See also: http://www.geneontology.org/GO.tools.shtml The developers of many of these tools hang out on the gofriends list, you may want to ask there too: gofriends at genome.stanford.edu On May 28, 2008, at 12:32 PM, Boris Steipe wrote: > A number of similarity measures on GO have been defined in the > literature. Once you have a PDB ID, get the corresponding UniProt ID, > then use FunSimMat to find other proteins of similar function. The > authors discuss the concepts and pitfalls of such an approach in > their 2007 NAR paper. > > http://funsimmat.bioinf.mpi-inf.mpg.de/ > > However this approach does not really operate on independent data: a > very large number of GO annotations is "inferred from electronic > annotation" - i.e. more or less from a BLAST search. You are likely > to get very similar information by simply doing a BLAST (or VAST) > search in the first place: homologous proteins have similar function. > But try it, it's quite informative. > > HTH, > Boris > > > On 28-May-08, at 2:37 PM, Xue Li wrote: > >> Hello all, >> >> Does anyone know whether I could use GO to identify functional >> similar >> proteins? Given a protein pdbID, can I search GO for functional >> similar proteins? Thanks. >> >> -- >> Xue, Li >> Bioinformatics and Computational Biology program @ ISU >> Ames, IA 50010 >> 515-450-7183 >> >> _______________________________________________ >> 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 hiekeen at gmail.com Wed May 28 21:23:00 2008 From: hiekeen at gmail.com (Jinyan Huang) Date: Thu, 29 May 2008 09:23:00 +0800 Subject: [BiO BB] How to get the special Transcription Factor target sequences? In-Reply-To: <3400.66.44.122.59.1211996127.squirrel@webmail.sibs.ac.cn> References: <701a2c50805271003r2dd3945cv67f3f28d1b10ef54@mail.gmail.com> <3400.66.44.122.59.1211996127.squirrel@webmail.sibs.ac.cn> Message-ID: Thank you very much for your suggestion. It is easy to registrate on gene-regulation.com. But when I browse the TRANSFAC database, it links to http://www.biobase-international.com/. For a free trial, it must finish a registration form. It is hard to pass this registration form. It is like this http://www.biobase-international.com/pages/index.php?id=456. In JARSPAR I can not find the factors which I interested no profiles in JASPAR satisfies search criteria 2008/5/29 lichunjiang : > > > Really? I registrated for gene-regulation.com a couple of years ago, it is > quite easy.?It does not make sense that you can not register. Or you > should just write to the service to fix the problem. > > Actually, > it is free to use a reduced version. For the full professional version, > you need to pay. > > Besides Transfac, I recommend another > database: JARSPAR available at http://jaspar.genereg.net/.?It is > totally free to use. > Hope this help. > Good luck! > > > >> It seems it is hard to pass the registration. >> >> 2008/5/28 J Greenbaum : >>> The > Transfac database (www.gene-regulation.com/pub/databases.html) >>> should have what you are looking for... >>> >>> Jason Greenbaum >>> Postdoctoral Fellow >>> > La Jolla Institute for Allergy & Immunology >>> >>> 2008/5/27 Jinyan Huang : >>>> I want to get the Transcription Factor target sequences. > They are >>>> > Oct4 $B!$ (BSox2 $B!$ (BcMyc $B!$ (BKlf4 $B!$ (BNanog $B!$ (BLin28. >>>> Is there such free database? Or should I just search it one > by one >>>> from the literature? >>>> >>>> >>>> -- >>>> Best regards, >>>> Jinyan Huang (ekeen) >>>> School of Life > Sciences and Technology, 1302 Room >>>> Tongji University >>>> Siping Road 1239, Shanghai 200092 >>>> P.R. > China >>>> Tel :0086-21-65981041 >>>> Msn: > hiekeen at hotmail.com >>>> eMail: hiekeen at gmail.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 >>> >> > >> >> >> -- >> Best regards, >> > Jinyan Huang (ekeen) >> School of Life Sciences and Technology, > 1302 Room >> Tongji University >> Siping Road 1239, Shanghai > 200092 >> P.R. China >> Tel :0086-21-65981041 >> Msn: > hiekeen at hotmail.com >> eMail: hiekeen at gmail.com >> >> _______________________________________________ >> BBB > mailing list >> BBB at bioinformatics.org >> > http://www.bioinformatics.org/mailman/listinfo/bbb >> >> > > > > -- > lichunjiang at sibs.ac.cn > Institute of > Biochemistry and Cell Biology, > Shanghai Institutes for Biological > Sciences, > Chinese Academy of Sciences > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > -- Best regards, Jinyan Huang (ekeen) School of Life Sciences and Technology, 1302 Room Tongji University Siping Road 1239, Shanghai 200092 P.R. China Tel :0086-21-65981041 Msn: hiekeen at hotmail.com eMail: hiekeen at gmail.com From me.lixue at gmail.com Thu May 29 12:06:41 2008 From: me.lixue at gmail.com (Xue Li) Date: Thu, 29 May 2008 11:06:41 -0500 Subject: [BiO BB] questions on blast Message-ID: <62ed16460805290906m48870015xa858e29b85630e1e@mail.gmail.com> Hello all, I installed blast-2.2.18 on my Ubuntu, and did blastp on 1RREQ_B.fasta.txt on pdb database. I got the following results: Score = 1147 bits (2967), Expect = 0.0, Method: Composition-based stats. Identities = 596/637 (93%), Positives = 596/637 (93%) Query: 1 SSTDQGTNPAXXXXXXXXXXXXAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60 SSTDQGTNPA AGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR Sbjct: 1 SSTDQGTNPADTDDLTPTTLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60 Would someone please tell me what do the Xs mean in the query sequence? Also, the results is different from the NCBI blast result. I downloaded pdb database today. Local Blast results show that there are 36, 353 sequences in pdbaa, while NCBI blast shows 36,476 sequences in pdb database. Even I installed blast-2.2.18, local Blast results show that I am using BLASTP2.2.17. NCBI shows that they are using blast-2.2.18+. Did I do something wrong? -- Xue, Li Bioinformatics and Computational Biology program @ ISU Ames, IA 50010 515-450-7183 From boris.steipe at utoronto.ca Thu May 29 13:27:35 2008 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Thu, 29 May 2008 13:27:35 -0400 Subject: [BiO BB] questions on blast In-Reply-To: <62ed16460805290906m48870015xa858e29b85630e1e@mail.gmail.com> References: <62ed16460805290906m48870015xa858e29b85630e1e@mail.gmail.com> Message-ID: <2D51D693-A0E8-491A-97B7-4CD465499246@utoronto.ca> > Would someone please tell me what do the Xs mean in the query > sequence? Filtered low-complexity sequence. B. (The BLAST manual can be highly recommended.) From cgaray at bu.edu Thu May 29 13:51:26 2008 From: cgaray at bu.edu (Christopher Garay) Date: Thu, 29 May 2008 13:51:26 -0400 Subject: [BiO BB] How to get the special Transcription Factor target sequences? In-Reply-To: References: <701a2c50805271003r2dd3945cv67f3f28d1b10ef54@mail.gmail.com> <3400.66.44.122.59.1211996127.squirrel@webmail.sibs.ac.cn> Message-ID: <196446400805291051u2bcfca85j722c5beae5518b6c@mail.gmail.com> It looks like you are an academic user, so I think that this site may be the one you want to use to register for transfac: http://www.gene-regulation.com/register Chris Garay On 5/28/08, Jinyan Huang wrote: > > Thank you very much for your suggestion. > > It is easy to registrate on gene-regulation.com. But when I browse the > TRANSFAC database, it links to http://www.biobase-international.com/. > For a free trial, it must finish a registration form. It is hard to > pass this registration form. It is like this > http://www.biobase-international.com/pages/index.php?id=456. > > > In JARSPAR I can not find the factors which I interested > > no profiles in JASPAR satisfies search criteria > > > > 2008/5/29 lichunjiang : > > > > > > > Really? I registrated for gene-regulation.com a couple of years ago, it > is > > quite easy.?It does not make sense that you can not register. Or you > > should just write to the service to fix the problem. > > > > Actually, > > it is free to use a reduced version. For the full professional version, > > you need to pay. > > > > Besides Transfac, I recommend another > > database: JARSPAR available at http://jaspar.genereg.net/.?It is > > totally free to use. > > Hope this help. > > Good luck! > > > > > > > >> It seems it is hard to pass the registration. > >> > >> 2008/5/28 J Greenbaum : > >>> The > > Transfac database (www.gene-regulation.com/pub/databases.html) > >>> should have what you are looking for... > >>> > >>> Jason Greenbaum > >>> Postdoctoral Fellow > >>> > > La Jolla Institute for Allergy & Immunology > >>> > >>> 2008/5/27 Jinyan Huang : > >>>> I want to get the Transcription Factor target sequences. > > They are > >>>> > > Oct4 $B!$ (BSox2 $B!$ (BcMyc $B!$ (BKlf4 $B!$ (BNanog $B!$ (BLin28. > >>>> Is there such free database? Or should I just search it one > > by one > >>>> from the literature? > >>>> > >>>> > >>>> -- > >>>> Best regards, > >>>> Jinyan Huang (ekeen) > >>>> School of Life > > Sciences and Technology, 1302 Room > >>>> Tongji University > >>>> Siping Road 1239, Shanghai 200092 > >>>> P.R. > > China > >>>> Tel :0086-21-65981041 > >>>> Msn: > > hiekeen at hotmail.com > >>>> eMail: hiekeen at gmail.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 > >>> > >> > > > >> > >> > >> -- > >> Best regards, > >> > > Jinyan Huang (ekeen) > >> School of Life Sciences and Technology, > > 1302 Room > >> Tongji University > >> Siping Road 1239, Shanghai > > 200092 > >> P.R. China > >> Tel :0086-21-65981041 > >> Msn: > > hiekeen at hotmail.com > >> eMail: hiekeen at gmail.com > >> > >> _______________________________________________ > >> BBB > > mailing list > >> BBB at bioinformatics.org > >> > > http://www.bioinformatics.org/mailman/listinfo/bbb > >> > >> > > > > > > > > -- > > lichunjiang at sibs.ac.cn > > Institute of > > Biochemistry and Cell Biology, > > Shanghai Institutes for Biological > > Sciences, > > Chinese Academy of Sciences > > > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > > -- > Best regards, > Jinyan Huang (ekeen) > School of Life Sciences and Technology, 1302 Room > Tongji University > Siping Road 1239, Shanghai 200092 > P.R. China > Tel :0086-21-65981041 > Msn: hiekeen at hotmail.com > eMail: hiekeen at gmail.com > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From xiaowei.jiang at msn.com Thu May 29 14:25:00 2008 From: xiaowei.jiang at msn.com (Xiaowei Jiang) Date: Thu, 29 May 2008 19:25:00 +0100 Subject: [BiO BB] questions on blast In-Reply-To: <62ed16460805290906m48870015xa858e29b85630e1e@mail.gmail.com> References: <62ed16460805290906m48870015xa858e29b85630e1e@mail.gmail.com> Message-ID: Hi XUE, You can simply turn the filter option off. By default, you have the following parameters set, when you use NCBI BLAST stand alone program. ------------------------------------------ blastall -p blastp -d nr -i stdin -e 10 -m 0 -o stdout -F T -G 11 -E 2 -X 15 -v 500 -b 250 -f 11 -g T -a 1 -M BLOSUM62 -W 3 -z 0 -K 0 -Y 0 -T F -U F -y 0.0 -Z 0 -A 40 ------------------------------------------- The option "-F" which filters the query sequence for low-complexity subsequences. You can simply turn this option off by using <-F "">. Please check NCBI BLAST documentation for detail! Regards, Xiaowei -------------------- Smurfit Institute of Genetics University of Dublin, Trinity College, Ireland -----Original Message----- From: bbb-bounces at bioinformatics.org [mailto:bbb-bounces at bioinformatics.org] On Behalf Of Xue Li Sent: 29 May 2008 17:07 To: General Forum at Bioinformatics.Org Subject: [BiO BB] questions on blast Hello all, I installed blast-2.2.18 on my Ubuntu, and did blastp on 1RREQ_B.fasta.txt on pdb database. I got the following results: Score = 1147 bits (2967), Expect = 0.0, Method: Composition-based stats. Identities = 596/637 (93%), Positives = 596/637 (93%) Query: 1 SSTDQGTNPAXXXXXXXXXXXXAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60 SSTDQGTNPA AGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR Sbjct: 1 SSTDQGTNPADTDDLTPTTLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60 Would someone please tell me what do the Xs mean in the query sequence? Also, the results is different from the NCBI blast result. I downloaded pdb database today. Local Blast results show that there are 36, 353 sequences in pdbaa, while NCBI blast shows 36,476 sequences in pdb database. Even I installed blast-2.2.18, local Blast results show that I am using BLASTP2.2.17. NCBI shows that they are using blast-2.2.18+. Did I do something wrong? -- Xue, Li Bioinformatics and Computational Biology program @ ISU Ames, IA 50010 515-450-7183 _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From marty.gollery at gmail.com Thu May 29 16:26:51 2008 From: marty.gollery at gmail.com (Martin Gollery) Date: Thu, 29 May 2008 13:26:51 -0700 Subject: [BiO BB] questions on blast In-Reply-To: <62ed16460805290906m48870015xa858e29b85630e1e@mail.gmail.com> References: <62ed16460805290906m48870015xa858e29b85630e1e@mail.gmail.com> Message-ID: Hi The X's are an indication that the sequence has been filtered for low complexity data by the filtering program SEG. Best regards, Marty On Thu, May 29, 2008 at 9:06 AM, Xue Li wrote: > Hello all, > > I installed blast-2.2.18 on my Ubuntu, and did blastp on > 1RREQ_B.fasta.txt on pdb database. > > I got the following results: > > Score = 1147 bits (2967), Expect = 0.0, Method: Composition-based stats. > Identities = 596/637 (93%), Positives = 596/637 (93%) > > Query: 1 SSTDQGTNPAXXXXXXXXXXXXAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60 > SSTDQGTNPA AGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR > Sbjct: 1 SSTDQGTNPADTDDLTPTTLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60 > > Would someone please tell me what do the Xs mean in the query sequence? > > Also, the results is different from the NCBI blast result. I > downloaded pdb database today. Local Blast results show that there are > 36, 353 sequences in pdbaa, while NCBI blast shows 36,476 sequences in > pdb database. > > Even I installed blast-2.2.18, local Blast results show that I am > using BLASTP2.2.17. NCBI shows that they are using blast-2.2.18+. > > Did I do something wrong? > > > -- > Xue, Li > Bioinformatics and Computational Biology program @ ISU > Ames, IA 50010 > 515-450-7183 > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- -- Martin Gollery Senior Bioinformatics Scientist TimeLogic- a Division of Active Motif 775-833-9113 880 Northwood Blvd. Suite 7 Incline Village, NV 89451 From silkhuang at gmail.com Thu May 29 19:18:00 2008 From: silkhuang at gmail.com (Huang Tao) Date: Thu, 29 May 2008 15:18:00 -0800 Subject: [BiO BB] questions on blast In-Reply-To: <62ed16460805290906m48870015xa858e29b85630e1e@mail.gmail.com> References: <62ed16460805290906m48870015xa858e29b85630e1e@mail.gmail.com> Message-ID: <5db67c690805291618s33e5d5b2m4c0739fa4869a7fa@mail.gmail.com> Xs mean gaps, which can be considered as 'insertion' or 'deletion' in biology. Btw, you may try BLAST service in RCSB PDB, you will find more hits. http://www.rcsb.org/pdb/search/searchSequence.do 2008/5/29 Xue Li : > Hello all, > > I installed blast-2.2.18 on my Ubuntu, and did blastp on > 1RREQ_B.fasta.txt on pdb database. > > I got the following results: > > Score = 1147 bits (2967), Expect = 0.0, Method: Composition-based stats. > Identities = 596/637 (93%), Positives = 596/637 (93%) > > Query: 1 SSTDQGTNPAXXXXXXXXXXXXAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60 > SSTDQGTNPA AGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR > Sbjct: 1 SSTDQGTNPADTDDLTPTTLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60 > > Would someone please tell me what do the Xs mean in the query sequence? > > Also, the results is different from the NCBI blast result. I > downloaded pdb database today. Local Blast results show that there are > 36, 353 sequences in pdbaa, while NCBI blast shows 36,476 sequences in > pdb database. > > Even I installed blast-2.2.18, local Blast results show that I am > using BLASTP2.2.17. NCBI shows that they are using blast-2.2.18+. > > Did I do something wrong? > > > -- > Xue, Li > Bioinformatics and Computational Biology program @ ISU > Ames, IA 50010 > 515-450-7183 > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- ??? Tao Huang From idh at poulet.org Fri May 30 07:40:18 2008 From: idh at poulet.org (Yannick Wurm) Date: Fri, 30 May 2008 13:40:18 +0200 Subject: [BiO BB] questions on blast In-Reply-To: <62ed16460805290906m48870015xa858e29b85630e1e@mail.gmail.com> References: <62ed16460805290906m48870015xa858e29b85630e1e@mail.gmail.com> Message-ID: <1E4614BD-0068-4BFC-A168-151CD350DC58@poulet.org> Hi Xue, the Xs are probably sequence that was filtered out... it could example be a "low complexity" repeat. Databases are constantly being updated... and sometimes there are several versions (with more or less redundancy). good luck, yannick ------------------------------------------- yannick . wurm @ unil . ch Ant Genomics, Ecology & Evolution @ Lausanne http://www.unil.ch/dee/page28685_fr.html On May 29, 2008, at 18:06 , Xue Li wrote: > Hello all, > > I installed blast-2.2.18 on my Ubuntu, and did blastp on > 1RREQ_B.fasta.txt on pdb database. > > I got the following results: > > Score = 1147 bits (2967), Expect = 0.0, Method: Composition- > based stats. > Identities = 596/637 (93%), Positives = 596/637 (93%) > > Query: 1 > SSTDQGTNPAXXXXXXXXXXXXAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60 > SSTDQGTNPA > AGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR > Sbjct: 1 > SSTDQGTNPADTDDLTPTTLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60 > > Would someone please tell me what do the Xs mean in the query > sequence? > > Also, the results is different from the NCBI blast result. I > downloaded pdb database today. Local Blast results show that there are > 36, 353 sequences in pdbaa, while NCBI blast shows 36,476 sequences in > pdb database. > > Even I installed blast-2.2.18, local Blast results show that I am > using BLASTP2.2.17. NCBI shows that they are using blast-2.2.18+. > > Did I do something wrong? > > > -- > Xue, Li > Bioinformatics and Computational Biology program @ ISU > Ames, IA 50010 > 515-450-7183 > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb From silkhuang at gmail.com Fri May 30 20:25:41 2008 From: silkhuang at gmail.com (Huang Tao) Date: Fri, 30 May 2008 16:25:41 -0800 Subject: [BiO BB] questions on blast In-Reply-To: <5db67c690805291618s33e5d5b2m4c0739fa4869a7fa@mail.gmail.com> References: <62ed16460805290906m48870015xa858e29b85630e1e@mail.gmail.com> <5db67c690805291618s33e5d5b2m4c0739fa4869a7fa@mail.gmail.com> Message-ID: <5db67c690805301725g99cd708wb30dbcc67dfcab8a@mail.gmail.com> Apparently, I make a mistake:) So, please omit it. 2008/5/29 Huang Tao : > Xs mean gaps, which can be considered as 'insertion' or 'deletion' in > biology. > > Btw, you may try BLAST service in RCSB PDB, you will find more hits. > http://www.rcsb.org/pdb/search/searchSequence.do > > > 2008/5/29 Xue Li : > > Hello all, >> >> I installed blast-2.2.18 on my Ubuntu, and did blastp on >> 1RREQ_B.fasta.txt on pdb database. >> >> I got the following results: >> >> Score = 1147 bits (2967), Expect = 0.0, Method: Composition-based >> stats. >> Identities = 596/637 (93%), Positives = 596/637 (93%) >> >> Query: 1 SSTDQGTNPAXXXXXXXXXXXXAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60 >> SSTDQGTNPA AGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR >> Sbjct: 1 SSTDQGTNPADTDDLTPTTLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR >> 60 >> >> Would someone please tell me what do the Xs mean in the query sequence? >> >> Also, the results is different from the NCBI blast result. I >> downloaded pdb database today. Local Blast results show that there are >> 36, 353 sequences in pdbaa, while NCBI blast shows 36,476 sequences in >> pdb database. >> >> Even I installed blast-2.2.18, local Blast results show that I am >> using BLASTP2.2.17. NCBI shows that they are using blast-2.2.18+. >> >> Did I do something wrong? >> >> >> -- >> Xue, Li >> Bioinformatics and Computational Biology program @ ISU >> Ames, IA 50010 >> 515-450-7183 >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > > > -- > ??? Tao Huang -- ??? Tao Huang From alexander.kel at biobase-international.com Sat May 31 00:08:19 2008 From: alexander.kel at biobase-international.com (Alexander Kel) Date: Sat, 31 May 2008 06:08:19 +0200 Subject: [BiO BB] How to get the special Transcription Factor target sequences? In-Reply-To: References: <701a2c50805271003r2dd3945cv67f3f28d1b10ef54@mail.gmail.com> <3400.66.44.122.59.1211996127.squirrel@webmail.sibs.ac.cn> Message-ID: <89c69d9b0805302108u13321a9dy331666b151df628b@mail.gmail.com> Hi all, To use the free public TRANSFAC please, click at: http://www.gene-regulation.com/pub/databases.html on the third item in the list: "Search TRANSFAC Public" http://www.gene-regulation.com/cgi-bin/pub/databases/transfac/search.cgi Sorry, for the confusion. Our sales and marketing made a good effort to put the Transfac professional at the top of the list :) But still the public version is available. Alexander On Thu, May 29, 2008 at 3:23 AM, Jinyan Huang wrote: > Thank you very much for your suggestion. > > It is easy to registrate on gene-regulation.com. But when I browse the > TRANSFAC database, it links to http://www.biobase-international.com/. > For a free trial, it must finish a registration form. It is hard to > pass this registration form. It is like this > http://www.biobase-international.com/pages/index.php?id=456. > > > In JARSPAR I can not find the factors which I interested > > no profiles in JASPAR satisfies search criteria > > > > 2008/5/29 lichunjiang : >> >> >> Really? I registrated for gene-regulation.com a couple of years ago, it is >> quite easy.?It does not make sense that you can not register. Or you >> should just write to the service to fix the problem. >> >> Actually, >> it is free to use a reduced version. For the full professional version, >> you need to pay. >> >> Besides Transfac, I recommend another >> database: JARSPAR available at http://jaspar.genereg.net/.?It is >> totally free to use. >> Hope this help. >> Good luck! >> >> >> >>> It seems it is hard to pass the registration. >>> >>> 2008/5/28 J Greenbaum : >>>> The >> Transfac database (www.gene-regulation.com/pub/databases.html) >>>> should have what you are looking for... >>>> >>>> Jason Greenbaum >>>> Postdoctoral Fellow >>>> >> La Jolla Institute for Allergy & Immunology >>>> >>>> 2008/5/27 Jinyan Huang : >>>>> I want to get the Transcription Factor target sequences. >> They are >>>>> >> Oct4 $B!$ (BSox2 $B!$ (BcMyc $B!$ (BKlf4 $B!$ (BNanog $B!$ (BLin28. >>>>> Is there such free database? Or should I just search it one >> by one >>>>> from the literature? >>>>> >>>>> >>>>> -- >>>>> Best regards, >>>>> Jinyan Huang (ekeen) >>>>> School of Life >> Sciences and Technology, 1302 Room >>>>> Tongji University >>>>> Siping Road 1239, Shanghai 200092 >>>>> P.R. >> China >>>>> Tel :0086-21-65981041 >>>>> Msn: >> hiekeen at hotmail.com >>>>> eMail: hiekeen at gmail.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 >>>> >>> >> >>> >>> >>> -- >>> Best regards, >>> >> Jinyan Huang (ekeen) >>> School of Life Sciences and Technology, >> 1302 Room >>> Tongji University >>> Siping Road 1239, Shanghai >> 200092 >>> P.R. China >>> Tel :0086-21-65981041 >>> Msn: >> hiekeen at hotmail.com >>> eMail: hiekeen at gmail.com >>> >>> _______________________________________________ >>> BBB >> mailing list >>> BBB at bioinformatics.org >>> >> http://www.bioinformatics.org/mailman/listinfo/bbb >>> >>> >> >> >> >> -- >> lichunjiang at sibs.ac.cn >> Institute of >> Biochemistry and Cell Biology, >> Shanghai Institutes for Biological >> Sciences, >> Chinese Academy of Sciences >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> >> > > > > -- > Best regards, > Jinyan Huang (ekeen) > School of Life Sciences and Technology, 1302 Room > Tongji University > Siping Road 1239, Shanghai 200092 > P.R. China > Tel :0086-21-65981041 > Msn: hiekeen at hotmail.com > eMail: hiekeen at gmail.com > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Alexander Kel, PhD SVP R&D BIOBASE GmbH, Halchtersche Strasse 33 D-38304 Wolfenbuettel Phone: +49 (0) 5331-8584-41 Fax: +49 (0) 5331-8584-70 www.biobase.de