From dibyadeep from gmail.com Fri Nov 2 05:17:46 2007 From: dibyadeep from gmail.com (Dibyadeep Paul) Date: Fri Nov 2 07:42:52 2007 Subject: [Bio-software] software for molecular modelling Message-ID: Hiii.. I am actually new to this sort of molecular modelling. I am trying to insert a protein into a cnt, and then run some simulations. I have the protein and cnt .pdb files, but am not able to understand which program to use to combine them together, and get a visual picture, so that I can be sure that the protein fits properly. I tried vmd, however it seems vmd only gives a visual picture, however doesn't exactly change the molecular coordinates. Could you kindly inform me as to which software I could use for such a job? Sincerely Dibyadeep From mzargh from yahoo.ca Thu Nov 8 12:36:20 2007 From: mzargh from yahoo.ca (Maryam) Date: Thu Nov 8 12:53:16 2007 Subject: [Bio-software] Prediction of surface property of the protein Message-ID: <885655.99045.qm@web88204.mail.re2.yahoo.com> Hi I was wondering if there is any software available to predict the surface property of the protein based on primary sequence. Thanks From harianto from mailer.sb.fsu.edu Fri Nov 9 12:33:43 2007 From: harianto from mailer.sb.fsu.edu (Harianto Tjong) Date: Fri Nov 9 13:31:20 2007 Subject: [Bio-software] Re: Bio-soft Digest, Vol 30, Issue 3 In-Reply-To: <200711091704.lA9H4DY17558@net.bio.net> References: <200711091704.lA9H4DY17558@net.bio.net> Message-ID: If you mean the solvent accessibility, you can try http://pipe.scs.fsu.eduand choose WESA. Hi > I was wondering if there is any software available to predict the > surface property of the protein based on primary sequence. > Thanks ------------------------------ > > _______________________________________________ > Bio-soft mailing list > Bio-soft@net.bio.net > http://www.bio.net/biomail/listinfo/bio-soft > > End of Bio-soft Digest, Vol 30, Issue 3 > *************************************** > -- Harianto Tjong Physics Grad Student Florida State University Tallahassee, FL 32306 Tel : (850) 645-1334 Fax : (850) 644-7244 http://people.scs.fsu.edu/~harianto From abhisheknayak28 from gmail.com Thu Nov 15 00:50:24 2007 From: abhisheknayak28 from gmail.com (abhisheknayak28@gmail.com) Date: Thu Nov 15 11:11:41 2007 Subject: [Bio-software] Re: Bio-soft Digest, Vol 29, Issue 7 References: <200710291704.l9TH4GY07346@net.bio.net> Message-ID: <07231e85-b8ab-47d5-875a-d0847c291b8e@d21g2000prf.googlegroups.com> Dear Amit Thanks for the reply , but the link which you have mentioned have the code written in java and pearl , and as I have already mentioned that I need the code written only in c++ Regards, Abhishek Amit Dattatreya Parhar wrote: > Blast Output parser in C++ > > Dear Abhishek, > > There are many blast parsers available . Here are the links for codes in > JAVA, C and PERL > > http://www.hip.harvard.edu/informatics/programs/JAVA%20BLAST%20Parser.html > > http://bioinfo.iq.usp.br/zerg/ > > http://www.bios.niu.edu/johns/bioinform/perl_blast_parser.htm > > Amit > Bioinformatics Analyst > amit.p@ocimumbio.com > > > ----- Original Message ----- > From: > To: > Sent: Monday, October 29, 2007 10:34 PM > Subject: Bio-soft Digest, Vol 29, Issue 7 > > > > 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. Blast Output parser in C++ (Abhishek Nayak) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 29 Oct 2007 12:24:29 +0530 > > From: Abhishek Nayak > > Subject: [Bio-software] Blast Output parser in C++ > > To: bio-soft@magpie.bio.indiana.edu > > Message-ID: <1193640869.2894.20.camel@localhost.localdomain> > > Content-Type: text/plain > > > > Hi, > > Dose anyone knows of a Blast output Parser whose source code is > > written in C++ and is a open source. > > I am in great need of it. If anyone knows of it please reply back. > > > > Regards, > > Abhishek Nayak > > > > > > ------------------------------ > > > > _______________________________________________ > > Bio-soft mailing list > > Bio-soft@net.bio.net > > http://www.bio.net/biomail/listinfo/bio-soft > > > > End of Bio-soft Digest, Vol 29, Issue 7 > > *************************************** From amit.p from ocimumbio.com Thu Nov 15 23:49:08 2007 From: amit.p from ocimumbio.com (Amit Dattatreya Parhar) Date: Fri Nov 16 10:27:46 2007 Subject: [Bio-software] Re: Bio-soft Digest, Vol 30, Issue 5 References: <200711151704.lAFH4LY04003@net.bio.net> Message-ID: <007b01c8280c$06af9cf0$fc01a8c0@ocimumbio.net> Visit NCBI FTP site and browser to NCBI toolkit. its open source and written in C++ . download it. I guess there is blast parser in there. regards, Amit ----- Original Message ----- From: To: Sent: Thursday, November 15, 2007 10:34 PM Subject: Bio-soft Digest, Vol 30, Issue 5 > 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: Bio-soft Digest, Vol 29, Issue 7 (abhisheknayak28@gmail.com) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 14 Nov 2007 21:50:24 -0800 (PST) > From: abhisheknayak28@gmail.com > Subject: [Bio-software] Re: Bio-soft Digest, Vol 29, Issue 7 > To: bionet-software@moderators.isc.org > Message-ID: > <07231e85-b8ab-47d5-875a-d0847c291b8e@d21g2000prf.googlegroups.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Amit > > Thanks for the reply , but the link which you have mentioned have the > code written in java and pearl , and as I have already mentioned that > I need the code written only in c++ > > Regards, > Abhishek > > Amit Dattatreya Parhar wrote: > > Blast Output parser in C++ > > > > Dear Abhishek, > > > > There are many blast parsers available . Here are the links for codes in > > JAVA, C and PERL > > > > http://www.hip.harvard.edu/informatics/programs/JAVA%20BLAST%20Parser.html > > > > http://bioinfo.iq.usp.br/zerg/ > > > > http://www.bios.niu.edu/johns/bioinform/perl_blast_parser.htm > > > > Amit > > Bioinformatics Analyst > > amit.p@ocimumbio.com > > > > > > ----- Original Message ----- > > From: > > To: > > Sent: Monday, October 29, 2007 10:34 PM > > Subject: Bio-soft Digest, Vol 29, Issue 7 > > > > > > > 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. Blast Output parser in C++ (Abhishek Nayak) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Mon, 29 Oct 2007 12:24:29 +0530 > > > From: Abhishek Nayak > > > Subject: [Bio-software] Blast Output parser in C++ > > > To: bio-soft@magpie.bio.indiana.edu > > > Message-ID: <1193640869.2894.20.camel@localhost.localdomain> > > > Content-Type: text/plain > > > > > > Hi, > > > Dose anyone knows of a Blast output Parser whose source code is > > > written in C++ and is a open source. > > > I am in great need of it. If anyone knows of it please reply back. > > > > > > Regards, > > > Abhishek Nayak > > > > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > Bio-soft mailing list > > > Bio-soft@net.bio.net > > > http://www.bio.net/biomail/listinfo/bio-soft > > > > > > End of Bio-soft Digest, Vol 29, Issue 7 > > > *************************************** > > > > ------------------------------ > > _______________________________________________ > Bio-soft mailing list > Bio-soft@net.bio.net > http://www.bio.net/biomail/listinfo/bio-soft > > End of Bio-soft Digest, Vol 30, Issue 5 > *************************************** > From msmith from eng.uiowa.edu Tue Nov 27 11:13:33 2007 From: msmith from eng.uiowa.edu (Mike Smith) Date: Tue Nov 27 11:16:35 2007 Subject: [Bio-software] Free gene browser Message-ID: <474C422D.9020902@eng.uiowa.edu> I thought this new tool might be of interest to this list. There is a free gene browser available from Bio::Neos, called GANT. It is a standalone application that lets you search for a gene and view the sequence, structure and annotation. The annotation is loaded from public data sources but the application is pluggable so as new plugins are developed for data sources you can just download the new plugin and view the annotation. There is also a primer picking capability that interfaces to an optimized Primer3 server. It is a nice interface for picking primers, you just click the sequence you want to amplify and select Pick Primers from the menu. It is fast also, you can design primers for a whole gene in less than a minute. The software is free and can be downloaded from http://gant.bioneos.com. Hope this is useful for some of you!