From akhtung from gmail.com Tue Jun 3 03:10:50 2008 From: akhtung from gmail.com (akhtung@gmail.com) Date: Tue Jun 3 11:02:45 2008 Subject: [Bio-software] CSV: Software for Mining and Visualizing Cohesive Subgraphs Message-ID: <44b53aa4-5f6b-4bc3-8cd4-0f10de71e8d0@x1g2000prh.googlegroups.com> Dear all, It is our pleasure to announce our latest software release for cohesive subgraph visualization available for download at: http://www.comp.nus.edu.sg/~atung/csv_binary.zip This is an implementation of our algorithm described in [1] and have potential application for visualizing large graphs like social network, protein-protein interaction graphs etc. Future update to CSV will be released through the mailing group: http://groups.google.com/group/nusminer Questions on CSV can be discussed at the forum there as well. Regards, Anthony Tung www.comp.nus.edu.sg/~atung [1] Nan Wang, Srinivasan Parthasarathy, Kian-Lee Tan, Anthony K. H. Tung. "CSV: Visualizing and Mining Cohesive Subgraphs". Accepted and to appear in ACM SIGMOD'08, Vancouver, Canada. http://www.comp.nus.edu.sg/~atung/publication/sigmod08_csv.pdf From sanjaysingh765 from gmail.com Mon Jun 9 05:01:28 2008 From: sanjaysingh765 from gmail.com (chunnu) Date: Mon Jun 9 11:33:21 2008 Subject: [Bio-software] a query Message-ID: <611c0632-6283-4a5d-9831-1e3987f5e15d@r37g2000prm.googlegroups.com> hi there, i am looking for a reliable software for batch seuence blast.plz help me regards sanjay From vlaleb from gmail.com Fri Jun 20 09:14:28 2008 From: vlaleb from gmail.com (vlaleb@gmail.com) Date: Fri Jun 20 11:04:38 2008 Subject: [Bio-software] FreezerPro - Complete Software Solution To Sample Tracking For Cryogenic Storage Message-ID: Dear all, It is our pleasure to announce FreezerPro - the best available frozen samples tracking software indispensable to any modern scientific or pharmaceutical laboratory. FreezerPro is a fast, reliable, and secure solution to managing all sample data. Know precisely where a frozen sample is located even before opening the freezer door. FreezerPro allows scientists and managers in research laboratories and pharmaceutical companies to inventory and retrieve frozen laboratory samples, bringing laboratory record keeping efficiency up to the highest level! FreezerPro is a desktop-like client-server application for the web, with its clients being a Microsoft Internet Explorer, FireFox, Camino, Safari or any other web browser on Windows, Mac and Linux platforms. Our front-end component is built with Ext JS - a client-side, JavaScript framework for building web applications. Our server component is built with Ruby On Rails and our proprietary ElegantDS engine and may be installed on anything from Windows to UNIX to Linux. The database component may utilize any relational database including MySQL, PostgreSQL, Oracle, SQL Server and DB2. http://www.freezerpro.com Best Regards, Vlad Lebedev www.ruro.com From indiasweden from gmail.com Tue Jun 24 10:17:26 2008 From: indiasweden from gmail.com (Googlefan) Date: Tue Jun 24 10:31:43 2008 Subject: [Bio-software] EBOX motif analysis Message-ID: <0a6b0aa6-084d-4e01-b1c0-cf442e4ca86b@d1g2000hsg.googlegroups.com> Hello, I want to analyse E-BOX ( CANNTG) motif in my sequence. Could you please tell me any tool to analyse it. Thanks Shobhit From krishna.aneesh from gmail.com Tue Jun 24 23:43:34 2008 From: krishna.aneesh from gmail.com (Aneesh Krishna) Date: Wed Jun 25 02:05:05 2008 Subject: [Bio-software] EBOX motif analysis In-Reply-To: <0a6b0aa6-084d-4e01-b1c0-cf442e4ca86b@d1g2000hsg.googlegroups.com> References: <0a6b0aa6-084d-4e01-b1c0-cf442e4ca86b@d1g2000hsg.googlegroups.com> Message-ID: <9cb9dfd70806242143v5cbf817aveff22ba1c7a6cff5@mail.gmail.com> Hi Shobit, To locate or search for any kind of such patterns there are online tools available. There are tools which take in the pattern as a regular expression and looks for the pattern in the input sequence. You can use DREG (http://bioinfo.hku.hk/EMBOSS/) This is a part of NUCLEIC MOTIFS in the EMBOSS package. The program requires 2 input. 1. Input Sequence: The user's sequence 2. Regular expression pattern: CA[CG][CG]TG The output will locate the positions of the E-box in the input sequence. I hope this will serve the purpose. On 6/24/08, Googlefan wrote: > > Hello, I want to analyse E-BOX ( CANNTG) motif in my sequence. Could > you please tell me any tool to analyse it. > Thanks > Shobhit > > _______________________________________________ > Bio-soft mailing list > Bio-soft@net.bio.net > http://www.bio.net/biomail/listinfo/bio-soft > -- Aneesh.K Associate-Life Sciences Mascon Global Limited Delhi Mob: 09999061058 From yanlinlin82 from gmail.com Wed Jun 25 11:31:18 2008 From: yanlinlin82 from gmail.com (Linlin Yan) Date: Wed Jun 25 11:40:42 2008 Subject: [Bio-software] Which amino acid residue does the letter 'J' mean? Message-ID: I just found there is a letter 'J' in NCBI's scoring matrix file (e.g. /usr/share/ncbi/data/BLOSUM50). Does anybody know what it is? Thanks! From yanlinlin82 from gmail.com Thu Jun 26 05:29:34 2008 From: yanlinlin82 from gmail.com (Linlin Yan) Date: Thu Jun 26 10:37:50 2008 Subject: [Bio-software] Which amino acid residue does the letter 'J' mean? In-Reply-To: <9cb9dfd70806252235w2ba7d3a9ke5af97f13f8c4734@mail.gmail.com> References: <9cb9dfd70806252235w2ba7d3a9ke5af97f13f8c4734@mail.gmail.com> Message-ID: <8d4c23b10806260329w68172ba3x302df6b40ffd4021@mail.gmail.com> Thank you for your answer. I searched by google right now, and got the link from NCBI: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/data/BLOSUM50 There's a 'J' letter. I haven't found the explaination yet. On Thu, Jun 26, 2008 at 1:35 PM, Aneesh Krishna wrote: > There is no 'J' in the scoring matrix that I found. Please go through the > below link. > > http://stardec.ascc.neu.edu/~bba/CBIO3580/ALIGN/blosum50.txt > > Can u tell detail? > > On 6/25/08, Linlin Yan wrote: >> >> I just found there is a letter 'J' in NCBI's scoring matrix file >> (e.g. /usr/share/ncbi/data/BLOSUM50). Does anybody know what it is? >> Thanks! >> >> _______________________________________________ >> Bio-soft mailing list >> Bio-soft@net.bio.net >> http://www.bio.net/biomail/listinfo/bio-soft > > > > -- > Aneesh.K > Associate-Life Sciences > Mascon Global Limited > Delhi > Mob: 09999061058 From raoul.fleck12man from comcast.com Thu Jun 26 17:34:55 2008 From: raoul.fleck12man from comcast.com (Raoul Fleckman) Date: Thu Jun 26 17:51:34 2008 Subject: [Bio-software] Re: Which amino acid residue does the letter 'J' mean? References: Message-ID: Leucine or Isoleucine On 2008-06-25, Linlin Yan wrote: > I just found there is a letter 'J' in NCBI's scoring matrix file > (e.g. /usr/share/ncbi/data/BLOSUM50). Does anybody know what it is? > Thanks! > From harianto from mailer.sb.fsu.edu Fri Jun 27 12:52:27 2008 From: harianto from mailer.sb.fsu.edu (Harianto Tjong) Date: Fri Jun 27 13:23:28 2008 Subject: [Bio-software] Re: Bio-soft Digest, Vol 37, Issue 7 In-Reply-To: <200806271703.m5RH3RO27489@net.bio.net> References: <200806271703.m5RH3RO27489@net.bio.net> Message-ID: I think J=W ( or Trp). For some purpose, amino acids are coded into the first 20 letters of alphabet, so after the 20th in alphabetical order (T=Threonine), there are 3 amino acids need to be mapped to fit: V,W,Y into B,J,O (for Val, Trp, Tyr). Maybe others can correct me if I'm wrong. On Fri, Jun 27, 2008 at 1:03 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: Which amino acid residue does the letter 'J' mean? > (Raoul Fleckman) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 26 Jun 2008 17:34:55 -0500 > From: Raoul Fleckman > Subject: [Bio-software] Re: Which amino acid residue does the letter > 'J' mean? > To: bionet-software@moderators.isc.org > Message-ID: > > Leucine or Isoleucine > > On 2008-06-25, Linlin Yan wrote: > > I just found there is a letter 'J' in NCBI's scoring matrix file > > (e.g. /usr/share/ncbi/data/BLOSUM50). Does anybody know what it is? > > Thanks! > > > > > > ------------------------------ > > _______________________________________________ > Bio-soft mailing list > Bio-soft@net.bio.net > http://www.bio.net/biomail/listinfo/bio-soft > > End of Bio-soft Digest, Vol 37, Issue 7 > *************************************** > -- Harianto Tjong 419 IMB Florida State University Tallahassee, FL 32306 Tel : (850) 645-1334 Fax : (850) 644-7244 http://people.scs.fsu.edu/~harianto From yanlinlin82 from gmail.com Fri Jun 27 21:03:41 2008 From: yanlinlin82 from gmail.com (Linlin Yan) Date: Fri Jun 27 21:44:44 2008 Subject: [Bio-software] Re: Bio-soft Digest, Vol 37, Issue 7 References: <200806271703.m5RH3RO27489@net.bio.net> Message-ID: On Jun 28, 1:52?am, "Harianto Tjong" wrote: > I think J=W ( or Trp). > For some purpose, amino acids are coded into the first 20 letters of > alphabet, so after the 20th in alphabetical order ?(T=Threonine), there are > 3 amino acids need to be mapped to fit: V,W,Y into B,J,O (for Val, Trp, > Tyr). I'm afraid the map may be wrong. Usually B means Asp or Asn, but not Val. I haven't seen J or O letter before I found J in NCBI scoring matrix. I guess Raoul Fleckman must be right: J means Leu or Ile. Need to be reassured. > Maybe others can correct me if I'm wrong. > > On Fri, Jun 27, 2008 at 1:03 PM, > wrote: > > > > > Send Bio-soft mailing list submissions to > > ? ? ? ?bio-s...@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-requ...@net.bio.net > > > You can reach the person managing the list at > > ? ? ? ?bio-soft-ow...@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: Which amino acid residue does the letter 'J' ?mean? > > ? ? ?(Raoul Fleckman) > > > ---------------------------------------------------------------------- > > > Message: 1 > > Date: Thu, 26 Jun 2008 17:34:55 -0500 > > From: Raoul Fleckman > > Subject: [Bio-software] Re: Which amino acid residue does the letter > > ? ? ? ?'J' ? ? mean? > > To: bionet-softw...@moderators.isc.org > > Message-ID: > > > Leucine or Isoleucine > > > On 2008-06-25, Linlin Yan wrote: > > > I just found there is a letter 'J' in NCBI's scoring matrix file > > > (e.g. /usr/share/ncbi/data/BLOSUM50). Does anybody know what it is? > > > Thanks! > > > ------------------------------ > > > _______________________________________________ > > Bio-soft mailing list > > Bio-s...@net.bio.net > >http://www.bio.net/biomail/listinfo/bio-soft > > > End of Bio-soft Digest, Vol 37, Issue 7 > > *************************************** > > -- > Harianto Tjong > 419 IMB > Florida State University > Tallahassee, FL 32306 > Tel : (850) 645-1334 > Fax : (850) 644-7244http://people.scs.fsu.edu/~harianto From yanlinlin82 from gmail.com Mon Jun 30 09:45:42 2008 From: yanlinlin82 from gmail.com (Linlin Yan) Date: Mon Jun 30 10:57:36 2008 Subject: [Bio-software] Re: Which amino acid residue does the letter 'J' mean? In-Reply-To: <4868EC29.2020105@ebi.ac.uk> References: <200806271703.m5RH3RO27489@net.bio.net> <4868EC29.2020105@ebi.ac.uk> Message-ID: <8d4c23b10806300745jdda2bcai76d134cb16812bc8@mail.gmail.com> Hi everyone in newsgroup bionet.software, It's very kind of Hamish, who sent me a very detail explain for single letter amio-acid codes. I forward the mail to the newsgroup. Hope it could help someone else. On Mon, Jun 30, 2008 at 10:22 PM, Hamish McWilliam wrote: > Hi Linlin, > > A brief description of the meanings of the single letter amino-acid codes > can be found in the RESID FAQ (http://www.ebi.ac.uk/RESID/faq.html#q01). > > In short 'J' is used for cases where the residue can be leucine ('L') or > isoleucine ('I') and is a result of the use of mass-spec sequencing where > the 'L' and 'I' cannot be distinguished. The 'B' (aspartic acid or > asparagine) and 'Z' (glutamic acid or glutamine) codes have a similar > function in chemical sequencing. > > Note that 'O' (pyrrolysine) and 'U' (selenocysteine) are now appearing in > the sequence databases (see http://beta.uniprot.org/news/2008/02/26/release > and > http://www.ebi.ac.uk/embl/Documentation/Release_notes/relnotes89/relnotes.html#2.2). > Currently not enough is known about the substitution rates of these residues > for them to be included in the scoring matrices, so they are generally > handled as unknown residues ('X'). > > I hope this helps, > > Hamish