From rosellic from ohsu.edu Wed Jan 2 18:27:18 2008 From: rosellic from ohsu.edu (Charles Roselli) Date: Wed Jan 2 21:52:50 2008 Subject: [Bio-software] Pulsar/Cluster software available&In-Reply-To= Message-ID: I'm looking for pulse analysis software to analysis LH pulsatility in sheep samples. I came across your name on the web and was wondering if you have anything available. I'd appreciate any information you can give me on how to obtain such software. Thank you. Chuck Roselli, Ph.D. Professor Dept. Physiology & Pharmacology L334 Oregon Health & Science University 3181 SW Sam Jackson Park Road Portland, OR 97239-3098 phone 503-494-5837 fax 503-494-4352 rosellic@ohsu.edu From giladle from bgu.ac.il Tue Jan 8 07:08:37 2008 From: giladle from bgu.ac.il (Gilad Lehmann) Date: Tue Jan 8 12:33:07 2008 Subject: [Bio-software] Advice about DNA alignment Message-ID: Hello everybody, I need an advice. I want to align 30 homolog non-coding sequencess of about 1800bp length with low similarity. In addition to substitutions and gaps, these sequences contain short and long tandem repeats in several non-identical locations. Which software is optimal for such an alignment? is it clustlW? T-coffee? maybe other software? I would like to avoid using repeatmasker if possible so the software has to ignore the disrupting repeats. Thanks in advance, Gilad? From darek.kedra from gmail.com Tue Jan 8 14:44:07 2008 From: darek.kedra from gmail.com (darked) Date: Tue Jan 8 14:53:48 2008 Subject: [Bio-software] Re: Advice about DNA alignment References: Message-ID: <4d2d3699-50a5-4b47-b8f4-cdcf5ae0edfc@r60g2000hsc.googlegroups.com> On Jan 8, 12:08 pm, Gilad Lehmann wrote: > Hello everybody, I need an advice. > > I want to align 30 homolog non-coding sequencess of about 1800bp length with low similarity. In addition to substitutions and gaps, these sequences contain short and long tandem repeats in several non-identical locations. > > Which software is optimal for such an alignment? is it clustlW? T-coffee? maybe other software? > I would like to avoid using repeatmasker if possible so the software has to ignore the disrupting repeats. > > Thanks in advance, > Giladư Well, if you call them homolog than somehow you selected these sequences based on similarity, I assume. So if you deal with non- coding regions close to a gene you may include 'anchors' -> extend sequences to include i.e. coding exons. >Which software is optimal for such an alignment? is it clustlW? T-coffee? maybe other software? You will need something more advanced me thinks. Check this paper http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1431#B15 and Aubergine: http://zeus.cs.vu.nl/programs/aubergenewww/ Easy web-interface: MultiPipMaker http://pipmaker.bx.psu.edu/cgi-bin/multipipmaker Shameless plug: http://openwetware.org/wiki/Wikiomics:Bioinfo_tutorial#DNA_alignment Comments about tools accuracy/ease of use etc. will be greatly appreciated ;-) Darek Kedra http://openwetware.org/wiki/Wikiomics From hains from uow.edu.au Tue Jan 8 23:22:29 2008 From: hains from uow.edu.au (hains@uow.edu.au) Date: Tue Jan 8 23:57:36 2008 Subject: [Bio-software] Grouping of proteins by function/category Message-ID: <1c072af6-82fe-4efd-a7be-ac5a0f730b05@y5g2000hsf.googlegroups.com> Hi all, I have a rather long list of proteins (about 230) that I want to group based on the function of each protein, such as structural, cytoplasmic, growth factor, that kind of thing. I'm after general groupings for the proteins. Does anyone know of a database that has this kind of info that I can submit my AC codes in a batch and have the result spat out the other end? I know there are various databases that will have this kind of info, but is there an easier way than looking each protein up individually? Thanks, Peter From darek.kedra from gmail.com Wed Jan 9 07:30:33 2008 From: darek.kedra from gmail.com (darked) Date: Wed Jan 9 11:43:34 2008 Subject: [Bio-software] Re: Grouping of proteins by function/category References: Message-ID: On Jan 9, 4:22 am, "ha...@uow.edu.au" wrote: > Hi all, > > I have a rather long list of proteins (about 230) that I want to group > based on the function of each protein, such as structural, > cytoplasmic, growth factor, that kind of thing. I'm after general > groupings for the proteins. Does anyone know of a database that has > this kind of info that I can submit my AC codes in a batch and have > the result spat out the other end? > > I know there are various databases that will have this kind of info, > but is there an easier way than looking each protein up individually? > > Thanks, > > Peter Hi, it depends on how fine-grained output you need. As long as you stay within gene ontology terms try G:profiler http://biit.cs.ut.ee/gprofiler/ Best, Darek Kedra http://openwetware.org/wiki/Wikiomics From amit.p from ocimumbio.com Thu Jan 10 01:06:41 2008 From: amit.p from ocimumbio.com (Amit Dattatreya Parhar) Date: Thu Jan 10 08:13:08 2008 Subject: [Bio-software] Re: Bio-soft Digest, Vol 32, Issue 2 References: <200801091704.m09H49L21812@net.bio.net> Message-ID: <008301c8534e$f92c3e80$fc01a8c0@ocimumbio.net> Hello everybody, I need an advice. > > I want to align 30 homolog non-coding sequencess of about 1800bp length with low similarity. In addition to substitutions and gaps, these sequences contain short and long tandem repeats in several non-identical locations. > > Which software is optimal for such an alignment? is it clustlW? T-coffee? maybe other software? > I would like to avoid using repeatmasker if possible so the software has to ignore the disrupting repeats. > > Thanks in advance, > Gilad??Z check out his algorithm might be of help http://nar.oxfordjournals.org/cgi/content/full/34/20/5932 regards, Amit Parhar Ocimum Biosolutions ----- Original Message ----- From: To: Sent: Wednesday, January 09, 2008 10:34 PM Subject: Bio-soft Digest, Vol 32, Issue 2 > Send Bio-soft mailing list submissions to > bio-soft@net.bio.net > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bio.net/biomail/listinfo/bio-soft > or, via email, send a message with subject or body 'help' to > bio-soft-request@net.bio.net > > You can reach the person managing the list at > bio-soft-owner@net.bio.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bio-soft digest..." > > > Today's Topics: > > 1. Advice about DNA alignment (Gilad Lehmann) > 2. Re: Advice about DNA alignment (darked) > 3. Grouping of proteins by function/category (hains@uow.edu.au) > 4. Re: Grouping of proteins by function/category (darked) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 08 Jan 2008 12:08:37 GMT > From: Gilad Lehmann > Subject: [Bio-software] Advice about DNA alignment > To: bio-soft@magpie.bio.indiana.edu > Message-ID: > Content-Type: text/plain; charset=utf-8 > > Hello everybody, I need an advice. > > I want to align 30 homolog non-coding sequencess of about 1800bp length with low similarity. In addition to substitutions and gaps, these sequences contain short and long tandem repeats in several non-identical locations. > > Which software is optimal for such an alignment? is it clustlW? T-coffee? maybe other software? > I would like to avoid using repeatmasker if possible so the software has to ignore the disrupting repeats. > > Thanks in advance, > Gilad??Z > > > ------------------------------ > > Message: 2 > Date: Tue, 8 Jan 2008 11:44:07 -0800 (PST) > From: darked > Subject: [Bio-software] Re: Advice about DNA alignment > To: bionet-software@moderators.isc.org > Message-ID: > <4d2d3699-50a5-4b47-b8f4-cdcf5ae0edfc@r60g2000hsc.googlegroups.com> > Content-Type: text/plain; charset=windows-1256 > > On Jan 8, 12:08 pm, Gilad Lehmann wrote: > > Hello everybody, I need an advice. > > > > I want to align 30 homolog non-coding sequencess of about 1800bp length with low similarity. In addition to substitutions and gaps, these sequences contain short and long tandem repeats in several non-identical locations. > > > > Which software is optimal for such an alignment? is it clustlW? T-coffee? maybe other software? > > I would like to avoid using repeatmasker if possible so the software has to ignore the disrupting repeats. > > > > Thanks in advance, > > Gilad? > > Well, if you call them homolog than somehow you selected these > sequences based on similarity, I assume. So if you deal with non- > coding regions close to a gene you may include 'anchors' -> extend > sequences to include i.e. coding exons. > > >Which software is optimal for such an alignment? is it clustlW? T-coffee? maybe other software? > You will need something more advanced me thinks. > > Check this paper http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1431#B15 > and Aubergine: > http://zeus.cs.vu.nl/programs/aubergenewww/ > > Easy web-interface: MultiPipMaker > http://pipmaker.bx.psu.edu/cgi-bin/multipipmaker > > Shameless plug: > http://openwetware.org/wiki/Wikiomics:Bioinfo_tutorial#DNA_alignment > > Comments about tools accuracy/ease of use etc. will be greatly > appreciated ;-) > > Darek Kedra > http://openwetware.org/wiki/Wikiomics > > > > ------------------------------ > > Message: 3 > Date: Tue, 8 Jan 2008 20:22:29 -0800 (PST) > From: "hains@uow.edu.au" > Subject: [Bio-software] Grouping of proteins by function/category > To: bionet-software@moderators.isc.org > Message-ID: > <1c072af6-82fe-4efd-a7be-ac5a0f730b05@y5g2000hsf.googlegroups.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all, > > I have a rather long list of proteins (about 230) that I want to group > based on the function of each protein, such as structural, > cytoplasmic, growth factor, that kind of thing. I'm after general > groupings for the proteins. Does anyone know of a database that has > this kind of info that I can submit my AC codes in a batch and have > the result spat out the other end? > > I know there are various databases that will have this kind of info, > but is there an easier way than looking each protein up individually? > > Thanks, > > Peter > > > > ------------------------------ > > Message: 4 > Date: Wed, 9 Jan 2008 04:30:33 -0800 (PST) > From: darked > Subject: [Bio-software] Re: Grouping of proteins by function/category > To: bionet-software@moderators.isc.org > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > On Jan 9, 4:22 am, "ha...@uow.edu.au" wrote: > > Hi all, > > > > I have a rather long list of proteins (about 230) that I want to group > > based on the function of each protein, such as structural, > > cytoplasmic, growth factor, that kind of thing. I'm after general > > groupings for the proteins. Does anyone know of a database that has > > this kind of info that I can submit my AC codes in a batch and have > > the result spat out the other end? > > > > I know there are various databases that will have this kind of info, > > but is there an easier way than looking each protein up individually? > > > > Thanks, > > > > Peter > > Hi, > > it depends on how fine-grained output you need. As long as you stay > within gene ontology terms try G:profiler > http://biit.cs.ut.ee/gprofiler/ > > Best, > Darek Kedra > http://openwetware.org/wiki/Wikiomics > > > > ------------------------------ > > _______________________________________________ > Bio-soft mailing list > Bio-soft@net.bio.net > http://www.bio.net/biomail/listinfo/bio-soft > > End of Bio-soft Digest, Vol 32, Issue 2 > *************************************** From amit.p from ocimumbio.com Thu Jan 10 01:18:07 2008 From: amit.p from ocimumbio.com (Amit Dattatreya Parhar) Date: Thu Jan 10 08:13:16 2008 Subject: [Bio-software] Re: Bio-soft Digest, Vol 32, Issue 2 References: <200801091704.m09H49L21812@net.bio.net> Message-ID: <00b301c85350$90c41dc0$fc01a8c0@ocimumbio.net> Message: 3 > Date: Tue, 8 Jan 2008 20:22:29 -0800 (PST) > From: "hains@uow.edu.au" > Subject: [Bio-software] Grouping of proteins by function/category > To: bionet-software@moderators.isc.org > Message-ID: > <1c072af6-82fe-4efd-a7be-ac5a0f730b05@y5g2000hsf.googlegroups.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all, > > I have a rather long list of proteins (about 230) that I want to group > based on the function of each protein, such as structural, > cytoplasmic, growth factor, that kind of thing. I'm after general > groupings for the proteins. Does anyone know of a database that has > this kind of info that I can submit my AC codes in a batch and have > the result spat out the other end? > > I know there are various databases that will have this kind of info, > but is there an easier way than looking each protein up individually? > > Thanks, > > Peter > > Hello Peter, Try COGs database @NCBI. There is a tool called KOGNITOR regards, Amit Parhar Ocimum Biosolutions ----- Original Message ----- From: To: Sent: Wednesday, January 09, 2008 10:34 PM Subject: Bio-soft Digest, Vol 32, Issue 2 > Send Bio-soft mailing list submissions to > bio-soft@net.bio.net > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bio.net/biomail/listinfo/bio-soft > or, via email, send a message with subject or body 'help' to > bio-soft-request@net.bio.net > > You can reach the person managing the list at > bio-soft-owner@net.bio.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bio-soft digest..." > > > Today's Topics: > > 1. Advice about DNA alignment (Gilad Lehmann) > 2. Re: Advice about DNA alignment (darked) > 3. Grouping of proteins by function/category (hains@uow.edu.au) > 4. Re: Grouping of proteins by function/category (darked) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 08 Jan 2008 12:08:37 GMT > From: Gilad Lehmann > Subject: [Bio-software] Advice about DNA alignment > To: bio-soft@magpie.bio.indiana.edu > Message-ID: > Content-Type: text/plain; charset=utf-8 > > Hello everybody, I need an advice. > > I want to align 30 homolog non-coding sequencess of about 1800bp length with low similarity. In addition to substitutions and gaps, these sequences contain short and long tandem repeats in several non-identical locations. > > Which software is optimal for such an alignment? is it clustlW? T-coffee? maybe other software? > I would like to avoid using repeatmasker if possible so the software has to ignore the disrupting repeats. > > Thanks in advance, > Gilad??Z > > > ------------------------------ > > Message: 2 > Date: Tue, 8 Jan 2008 11:44:07 -0800 (PST) > From: darked > Subject: [Bio-software] Re: Advice about DNA alignment > To: bionet-software@moderators.isc.org > Message-ID: > <4d2d3699-50a5-4b47-b8f4-cdcf5ae0edfc@r60g2000hsc.googlegroups.com> > Content-Type: text/plain; charset=windows-1256 > > On Jan 8, 12:08 pm, Gilad Lehmann wrote: > > Hello everybody, I need an advice. > > > > I want to align 30 homolog non-coding sequencess of about 1800bp length with low similarity. In addition to substitutions and gaps, these sequences contain short and long tandem repeats in several non-identical locations. > > > > Which software is optimal for such an alignment? is it clustlW? T-coffee? maybe other software? > > I would like to avoid using repeatmasker if possible so the software has to ignore the disrupting repeats. > > > > Thanks in advance, > > Gilad? > > Well, if you call them homolog than somehow you selected these > sequences based on similarity, I assume. So if you deal with non- > coding regions close to a gene you may include 'anchors' -> extend > sequences to include i.e. coding exons. > > >Which software is optimal for such an alignment? is it clustlW? T-coffee? maybe other software? > You will need something more advanced me thinks. > > Check this paper http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1431#B15 > and Aubergine: > http://zeus.cs.vu.nl/programs/aubergenewww/ > > Easy web-interface: MultiPipMaker > http://pipmaker.bx.psu.edu/cgi-bin/multipipmaker > > Shameless plug: > http://openwetware.org/wiki/Wikiomics:Bioinfo_tutorial#DNA_alignment > > Comments about tools accuracy/ease of use etc. will be greatly > appreciated ;-) > > Darek Kedra > http://openwetware.org/wiki/Wikiomics > > > > ------------------------------ > > Message: 3 > Date: Tue, 8 Jan 2008 20:22:29 -0800 (PST) > From: "hains@uow.edu.au" > Subject: [Bio-software] Grouping of proteins by function/category > To: bionet-software@moderators.isc.org > Message-ID: > <1c072af6-82fe-4efd-a7be-ac5a0f730b05@y5g2000hsf.googlegroups.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all, > > I have a rather long list of proteins (about 230) that I want to group > based on the function of each protein, such as structural, > cytoplasmic, growth factor, that kind of thing. I'm after general > groupings for the proteins. Does anyone know of a database that has > this kind of info that I can submit my AC codes in a batch and have > the result spat out the other end? > > I know there are various databases that will have this kind of info, > but is there an easier way than looking each protein up individually? > > Thanks, > > Peter > > > > ------------------------------ > > Message: 4 > Date: Wed, 9 Jan 2008 04:30:33 -0800 (PST) > From: darked > Subject: [Bio-software] Re: Grouping of proteins by function/category > To: bionet-software@moderators.isc.org > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > On Jan 9, 4:22 am, "ha...@uow.edu.au" wrote: > > Hi all, > > > > I have a rather long list of proteins (about 230) that I want to group > > based on the function of each protein, such as structural, > > cytoplasmic, growth factor, that kind of thing. I'm after general > > groupings for the proteins. Does anyone know of a database that has > > this kind of info that I can submit my AC codes in a batch and have > > the result spat out the other end? > > > > I know there are various databases that will have this kind of info, > > but is there an easier way than looking each protein up individually? > > > > Thanks, > > > > Peter > > Hi, > > it depends on how fine-grained output you need. As long as you stay > within gene ontology terms try G:profiler > http://biit.cs.ut.ee/gprofiler/ > > Best, > Darek Kedra > http://openwetware.org/wiki/Wikiomics > > > > ------------------------------ > > _______________________________________________ > Bio-soft mailing list > Bio-soft@net.bio.net > http://www.bio.net/biomail/listinfo/bio-soft > > End of Bio-soft Digest, Vol 32, Issue 2 > *************************************** From gasilver from nmsu.edu Thu Jan 10 11:37:02 2008 From: gasilver from nmsu.edu (Gail Silver) Date: Thu Jan 10 12:29:04 2008 Subject: [Bio-software] Pulsar/Cluster software available Message-ID: <000001c853a7$071d8c80$77b37b80@njcf.ad.nmsu.edu> Dr. Lazarus, I am very interested in the PULSAR program you spoke about on the website. Can you give me any information about it or can I download it from you? "I have a package available to perform endocrine pulse analysis. Both Merriam and Wachter's PULSAR and Veldhuis' Cluster algorithms can be run over the same data sets. Compared to the only other implementations of these algorithms I have seen, this software is slick and very fast. It is available as beta test software and will be distributed as shareware eventually. Please email me if you are doing any quantities of PULSAR or Cluster analysis and if you are interested in beta testing. Also available is some simulation software for generating endocrine blood data from user supplied parameters. A two compartment decay model is included and a novel method of simulating the secretory burst waveform is included so you can have a range of skewed variations on a gaussian burst shape...." Gail Silver Department of Animal and Range Sciences MSC 3I, Knox Hall 328 2980 South Espina Street New Mexico State University Las Cruces, NM 88003 Office: 505 646 2492 gasilver@nmsu.edu From bernieb from duke.edu Tue Jan 15 09:28:14 2008 From: bernieb from duke.edu (Bernie Ball) Date: Tue Jan 15 09:44:02 2008 Subject: [Bio-software] LIMS development Message-ID: <4D572680-D6E8-4A50-8370-AA8C28831D16@duke.edu> Hi, I would like to put together a good database (Filemaker Pro) to track all of our tissue samples from receipt through nucleotide extraction, PCR, and sequencing. Does anyone have a current (non-commercial) version that they would be willing to share as a model? The database would only be used by 3-4 people over the next 3 years but would be a great method to ensure that we do not duplicate our efforts etc. I guess it would be a sort of mini-LIMS system without all of the features required for most applications. Any assistance will be greatly appreciated. From krishna.aneesh from gmail.com Wed Jan 16 00:11:42 2008 From: krishna.aneesh from gmail.com (Aneesh Krishna) Date: Wed Jan 16 12:22:38 2008 Subject: [Bio-software] LIMS development In-Reply-To: <4D572680-D6E8-4A50-8370-AA8C28831D16@duke.edu> References: <4D572680-D6E8-4A50-8370-AA8C28831D16@duke.edu> Message-ID: <9cb9dfd70801152111m704cdc01wbaba4c138e308e67@mail.gmail.com> *Hi,* * * *FreeLIMS*(R) is the professional open source LIMS (Laboratory Information Management System) that you can use for free!!! You can download it from http://www.freelims.com/?gclid=CMWp15fFs5ACFQFjMAodCw9rHw . Check is it useful for you. Regards Aneesh.K Associate-Life Sciences Mascon Global Limitted On 1/15/08, Bernie Ball wrote: > > Hi, > > I would like to put together a good database (Filemaker Pro) to track > all of our tissue samples from receipt through nucleotide extraction, > PCR, and sequencing. Does anyone have a current (non-commercial) > version that they would be willing to share as a model? The database > would only be used by 3-4 people over the next 3 years but would be a > great method to ensure that we do not duplicate our efforts etc. I > guess it would be a sort of mini-LIMS system without all of the > features required for most applications. > > Any assistance will be greatly appreciated. > > _______________________________________________ > Bio-soft mailing list > Bio-soft@net.bio.net > http://www.bio.net/biomail/listinfo/bio-soft > -- Aneesh.K From sanjaysingh765 from gmail.com Tue Jan 22 04:20:46 2008 From: sanjaysingh765 from gmail.com (chunnu) Date: Tue Jan 22 12:03:55 2008 Subject: [Bio-software] query Message-ID: Hi There, I m trying 2 build a theoretical of a protein but unfortunately the template 4 whole protein is not availabe in PDB so i build 3/4 th part of protein by compertive modelling while remaining by de novo method..now I want to ligate the backbone of the both model in order to generate a complete model.may I do it??if yes then how..plz suggest a proper method..my mail ID is sanjaysingh765@gmail.com regards sanjay From bioinformatics from carthagenomics.com Wed Jan 23 04:52:54 2008 From: bioinformatics from carthagenomics.com (CarthaGenomics AT) Date: Wed Jan 23 11:18:36 2008 Subject: [Bio-software] International Bioinformatics Workshop in Tunisia Message-ID: <20080123105254.BRB38639@mailbox1.gnet.tn> Dear Sirs, My name is Nouredine Ben Khalaf, from CarthaGenomics Advanced Technologies in Tunisia (http://www.carthagenomics.com). Our start up CarthaGenomics Advanced Technologies, organizes an International Bioinformatics Course in Tunisia, "Biological Data Integration and Sequence Analysis " , on April 15th, and we are looking for people who will be interested in giving a half-day presentation in one of the following items : Origin of biological data, data formats, properties and relevance of biological databases. Pairwise and multiple sequence alignment, search for homologous sequences in databases Gene prediction and genome annotation. Evolutionary analysis and tree construction. Motif and pattern detection in Biological sequences Comparative genomics. Analysis of duplicated regions in genomes The practical session of this workshop will be given by two of our collegues from EMBL. CarthaGenomics Advanced Technologies offer all accomodations for speakers and trainers during these 10 days workshop excepting the travel fees. Scientists interested in giving one course of the mentioned items are welcome to send an mail to bioinformatics@carthagenomics.com Additional information will be given for interested applicants. Very Best regards N.BenKhalaf ------------ RAN BioLinks CarthaGenomics Advanced Technologies 2, rue Ali Bach Hamba 1000 ? Tunis, TUNISIA T?l : +216 98 90 27 78 | +33 9 52 47 34 86 Fax : +216 71 77 52 89 www.carthagenomics.com From thulsen from gmail.com Thu Jan 24 07:41:55 2008 From: thulsen from gmail.com (thulsen@gmail.com) Date: Thu Jan 24 12:06:43 2008 Subject: [Bio-software] BioVenn - A web application for the comparison and visualization of biological lists using area-proportional Venn diagrams Message-ID: We designed an easy-to-use web application named BioVenn to summarize the overlap between two or three lists of identifiers, using area- proportional Venn diagrams. This very useful tool can be found at http://www.cmbi.ru.nl/biovenn Kind regards, Tim Hulsen. From gilbertd from net.bio.net Thu Jan 24 12:24:31 2008 From: gilbertd from net.bio.net (Don Gilbert) Date: Thu Jan 24 12:25:28 2008 Subject: [Bio-software] Re: BioVenn Message-ID: <200801241724.m0OHOVX10237@net.bio.net> Tim, This looks very nice and handy for many uses in biosciences. Here is my wish list for enhancements: - proved a "save as" option for the figure. Clicking on the diagram and choosing my browser's save frame source as is somewhat non-easy. - offer more than 3 sets. Sometimes we have a few more (4,5..) that can be usefully shown in a Venn diagram. - provide for upload of one table file with an ID field and classes fields; e.g. ID1 x y . ID2 . y . this of course is tricky as users can have their data in many formats. -- Don Gilbert -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@indiana.edu--http://marmot.bio.indiana.edu/ From jeedward from gmail.com Sun Jan 27 09:32:42 2008 From: jeedward from gmail.com (john) Date: Sun Jan 27 13:22:12 2008 Subject: [Bio-software] BCBGC-08 Final call for papers Message-ID: BCBGC-08 Final call for papers The 2008 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) (website: www.PromoteResearch.org ) will be held during July 7-10 2008 in Orlando, FL, USA. The draft paper submission deadline is February 4 2008. BCBGC brings together both academic and industrial scientists and developers from a diverse range of disciplines including bioinformatics, computer science, computational biology, genomics, proteomics and chemoinformatics. One of the main goals of the conference is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers in different fields. Papers that demonstrate applications of existing techniques or developments of new methods are equally welcomed to the conference. The conference will be held at the same time and location where some other major events will be taking place. The website contains more details. Sincerely John Edward From lacybm from infovia.com.ar Mon Jan 28 08:16:29 2008 From: lacybm from infovia.com.ar (LACYB MONTE) Date: Mon Jan 28 12:53:17 2008 Subject: [Bio-software] New free utility software for laboratories Message-ID: <000201c861b0$00095890$0e00000a@OFICINA> Hello, I am interested IN SOFT Labmain (Laboratory Maintenance Organiser), like I can make to acquire it. Thank you Carlos Falguera Lacyb Monte From krishna.aneesh from gmail.com Tue Jan 29 00:15:27 2008 From: krishna.aneesh from gmail.com (Aneesh Krishna) Date: Tue Jan 29 00:48:16 2008 Subject: [Bio-software] Free software for motif finding Message-ID: <9cb9dfd70801282115w5241b63cxfbb5887c8add804c@mail.gmail.com> Dear All, Please tell me some free software for finding motifs from a set of sequences (both nucleotide and protein). And I want to run it in windows and command line also. With Regards- Aneesh.K krishna.aneesh@gmail.com Mob: 09999061058 From darek.kedra from gmail.com Tue Jan 29 09:30:09 2008 From: darek.kedra from gmail.com (darked) Date: Tue Jan 29 09:42:49 2008 Subject: [Bio-software] Re: Free software for motif finding References: Message-ID: <6bfbaabc-3dfe-4da8-a17e-e9d744cf0459@c4g2000hsg.googlegroups.com> Hi, Take a look at: http://openwetware.org/wiki/Wikiomics:Sequence_motifs and: http://openwetware.org/wiki/Tregwiki save for MEME these will work on DNA sequences. Best, Darek Kedra http://openwetware.org/wiki/Wikiomics On Jan 29, 5:15 am, "Aneesh Krishna" wrote: > Dear All, > > Please tell me some free software for finding motifs from a set of sequences > (both nucleotide and protein). And I want to run it in windows and command > line also. > With Regards- > Aneesh.K > krishna.ane...@gmail.com > Mob: 09999061058 From ppuigbo from urv.cat Thu Jan 31 03:07:16 2008 From: ppuigbo from urv.cat (ppuigbo@urv.cat) Date: Thu Jan 31 09:10:07 2008 Subject: [Bio-software] E-CAI: web server to estimate an expected value of CodonAdaptation Index (eCAI) Message-ID: The E-CAI server is a web-application and an executable program that calculates the expected value of the Codon Adaptation Index (CAI) for a set of query sequences by generating random sequences with similar G+C content and amino acid composition to the input. This expected CAI therefore provides a direct threshold value for discerning whether the differences in the CAI value are statistically significant and arise from the codon preferences or whether they are merely artifacts that arise from internal biases in the G+C composition and/or amino acid composition of the query sequences. E-CAI is freely accessible at http://genomes.urv.cat/CAIcal/E-CAI For more details see the article Puigbo P, Bravo IG and Garcia-Vallv? S. E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI). BMC Bioinformatics 2008, 9:65