From Mike.Fursov from gmail.com Tue Oct 7 13:46:53 2008 From: Mike.Fursov from gmail.com (Mikhail Fursov) Date: Tue Oct 7 13:59:17 2008 Subject: [Bio-software] UGENE v1.2 released Message-ID: <49826b75-4790-4843-951b-61e17eb4eaf2@q26g2000prq.googlegroups.com> UGENE is a free and open-source cross-platform bioinformatics software package. The version 1.2 adds several new plugins, MacOS X platform support and dozens of performance, usability and compatibility improvements. The complete list of changes can be found here: http://ugene.unipro.ru/changelist.html Link to the site: http://ugene.unipro.ru From almurph from altavista.com Thu Oct 9 05:29:58 2008 From: almurph from altavista.com (almurph@altavista.com) Date: Thu Oct 9 10:51:42 2008 Subject: [Bio-software] Looping inside Needleman-Wunsch algorithm & good values for the Similairity Matrix Message-ID: <320ec4d7-8f21-42c9-ae8f-359e17ddf1a6@v30g2000hsa.googlegroups.com> Hi everyone, Concerning the Needleman-Wunsch algorithm (cf. http://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm) I have noticed a possible loop. Inside the algorithm there is an important decision making mechanism. Its a "if, else if, else if" structure like: if(ScoreValue == DiagonalValue + SimilarityValue(i, j) { blah; } else if(Score == Left + d) { blah; } else if(Score == Up + d) { blah; } I've been playing with value of the similarity matrix and for certain values I can get the algorithms to stick as there is no else clause to offer an out if none of the above conditions are met. Now I know that I could introuduce an else statement and avoid the loop but it does not address the fundamental probalm of constructing a useful Similarity matrix. It's on this point issue that I want to ask for help. The similaity Matrix that I built for my task is ultimately causing this problem. So i need to make it better. My question is: what properties should a good Similarity matrix have to avoid this loop? How does one go about constructing an effective Similarity matrix? What properties should it have? I'm not referring to the simple structure that score 1 for a match and 0 for a mismatch. i'm referring to more complex structures... Any hints/advice/user-experiences/websites/papers much appreciated. Thanking you, Al. From sanjaysingh765 from gmail.com Sat Oct 18 10:28:09 2008 From: sanjaysingh765 from gmail.com (chunnu) Date: Sat Oct 18 12:38:58 2008 Subject: [Bio-software] e-value Message-ID: <1af1a86f-3722-4f9e-9d09-d082971bd548@a18g2000pra.googlegroups.com> hi all, i have a set of arabidopsis genes ( approx. 100 ) and want to point out their orthologs from oryza sativa.Can anyone suggest me the best method to do this...I was thinking about reciprocal best Basic Local Alignment Search Tool hits (RBH) but I was confused about the parameters especially for e-value.Plz sugggest me the optimal e-value for oorthologs and homologs identification regards From info from noster-it.com Fri Oct 24 04:51:00 2008 From: info from noster-it.com (Dokorek) Date: Fri Oct 24 10:21:56 2008 Subject: [Bio-software] networking database for biologists Message-ID: <5ba5b69c-d453-4d0e-9c25-56c9df798c7c@m73g2000hsh.googlegroups.com> Join the Fastest Growing Bio Community - you know Facebook, Xing or MySpace, LinkedIn. In biology it exists as well: Visit academic portal http://biospace.ethz.ch register, confirm registration in email - join group, institute (if no exist - create your institution), create own group of interesst and share data, contacts, micorscope images, build network. You can be first and can create a future scientific group of interests. ETH Zuerich Team From thulsen from gmail.com Tue Oct 28 17:50:27 2008 From: thulsen from gmail.com (Tim Hulsen) Date: Tue Oct 28 18:06:10 2008 Subject: [Bio-software] Re: BioVenn In-Reply-To: <200801241721.m0OHLXv09231@net.bio.net> References: <200801241721.m0OHLXv09231@net.bio.net> Message-ID: <6c8101220810281550n6b85ed2av2438439345a32bf0@mail.gmail.com> Hi, BioVenn is now published in BMC Genomics: http://www.biomedcentral.com/1471-2164/9/488 Please also have a look at BioVenn's brother VennDiagram.tk, which takes numbers as input instead of lists of identifiers. regards, Tim Hulsen. On Thu, Jan 24, 2008 at 6:21 PM, Don Gilbert wrote: > > 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 inesdesantiago from gmail.com Thu Oct 30 10:43:11 2008 From: inesdesantiago from gmail.com (ines santiago) Date: Thu Oct 30 11:42:54 2008 Subject: [Bio-software] Re: Bio-soft Digest, Vol 41, Issue 5 In-Reply-To: <200810291703.m9TH3UV27032@net.bio.net> References: <200810291703.m9TH3UV27032@net.bio.net> Message-ID: <7f52bad90810300843s4a0adcdftcfffa48073941d25@mail.gmail.com> EXCELENT TOOL This is just what I needed. :) Thanks! Keep Up the good Work for the Authors! On Wed, Oct 29, 2008 at 5:03 PM, wrote: > 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. Re: BioVenn (Tim Hulsen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 28 Oct 2008 23:50:27 +0100 > From: "Tim Hulsen" > Subject: [Bio-software] Re: BioVenn > To: bio-soft@magpie.bio.indiana.edu > Message-ID: > <6c8101220810281550n6b85ed2av2438439345a32bf0@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > BioVenn is now published in BMC Genomics: > http://www.biomedcentral.com/1471-2164/9/488 > > Please also have a look at BioVenn's brother VennDiagram.tk, which takes > numbers as input instead of lists of identifiers. > > regards, > Tim Hulsen. > > On Thu, Jan 24, 2008 at 6:21 PM, Don Gilbert > wrote: > > > > > 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/ > > > > > ------------------------------ > > _______________________________________________ > Bio-soft mailing list > Bio-soft@net.bio.net > http://www.bio.net/biomail/listinfo/bio-soft > > End of Bio-soft Digest, Vol 41, Issue 5 > *************************************** > From parsonsl from upstate.edu Fri Oct 31 16:17:10 2008 From: parsonsl from upstate.edu (lparsons) Date: Fri Oct 31 16:49:54 2008 Subject: [Bio-software] SNP Analysis : Parser for Polybayes result In-Reply-To: <1150882311.332561.220910@m73g2000cwd.googlegroups.com> References: <1150813517.075792.171120@b68g2000cwa.googlegroups.com> <1150882311.332561.220910@m73g2000cwd.googlegroups.com> Message-ID: <20274161.post@talk.nabble.com> Hello I am the author of that web page, which is no longer up because the lab itself no longer exists. There should have been a redirect link back in 2006 when you wrote that message, however the redirect link itself would no longer work at this point. I have attached the perl script that was mentioned in the link, feel free to use it however you like. I apologize for not getting this to you sooner, hopefully someone can make use of this old script. http://www.nabble.com/file/p20274161/SNP_analysis.pl SNP_analysis.pl i.j.nijman wrote: > > forgotten link: http://www.ccgb.umn.edu/~lparsons/downloads/index.html > i.j.nijman@gmail.com wrote: >> Hi, >> >> Have you seen this page? There's a simple script which parses the >> polybayes output. >> >> Cheers, >> Ies Nijman >> >> Elango, Palchamy (ICRISAT-IN) wrote: >> > I am using Polybayes program [Author: Prof. Gabor T. Marth] for SNP >> analysis. >> > >> > I wish to parse and extract SNP associated information from the output >> (textual mulitple sequence alignment) of Polybayes program. >> > >> > Alternatively I am trying out the possibilities of converting the >> polybayes alignment output into any standard multiple alignment format, >> so that I can able to use other SNP analysis programs that read multiple >> sequence alignment files as input. >> > >> > I wish to use your parser script or any bioperl / biojava module. >> > Does anyone know or use any bioperl /biopython /biojava module ? >> > I shall be grateful if you could kindly provide me some tips or >> additional information on this. >> > >> > Thanking you >> > Elango >> > P.Elango >> > >> > GT-Biotechnology, >> > International Crops Research Institute for the Semi-Arid Tropics >> (ICRISAT), >> > Patancheru - 502 324, Andhra Pradesh, India. >> > Work: +(91) 40 307 13321 , Home: +(91) 40 559 98770 / +(91) 98854 >> 98770 (Mobile) >> > pelango@cgiar.org www.cgiar.org >> elango@palchamy.com > > _______________________________________________ > Bio-soft mailing list > Bio-soft@net.bio.net > http://www.bio.net/biomail/listinfo/bio-soft > > -- View this message in context: http://www.nabble.com/Re%3A-SNP-Analysis-%3A-Parser-for-Polybayes-result-tp4958969p20274161.html Sent from the Bio.net - Bio-soft mailing list archive at Nabble.com.