computational analysis of sequences

Mr Malay kumar Basu curiouser at ccmb.ap.nic.in
Fri Apr 6 11:14:30 EST 2001


Hi Sushma:

You can download Network BLAST from:
ftp://ncbi.nlm.nih.gov/blast/network/netblast/

There are binaries and executabls for different platforms. Check whether
it works in your case. Sometimes these clients gives troubles for
firewall. Check with one sequence and see it works. As this clients works
in command line mode, it is easy to wrap up the client into a script that
will execute the client repeatedly (check the Blast FAQ list, at what time
of the day you should send multiple request to the server) from a
directory conataining your input sequences. Contact me if you require any
further help.

Best of luck,

Malay

On Fri, 6 Apr 2001, S.Tiwari wrote:

> Hi malay,
>     I would hopefully have thousands of clone sequence to do blast with so a
> batch blast would really be helpfull,
> Please let me know how i could do it, you must have realised that I am ignorant
> about the computational depths as I have never done it before,
> thanks alot for the help,
> sushma
> 
> Malay wrote:
> 
> > You could use NCBI network blast client. I am not sure whether it still
> > works. If you want to use cut and paste you can use
> > SeWeR(http://iubio.bio.indiana.edu/webapps/SeWeR/). It opens each search at
> > separate window.
> >
> > By the way if there are enough demands please let me know I can hack a Perl
> > script for Batch mode blast.
> >
> > Malay
> >
> > Malay Kumar Basu
> > Centre for Cellular and Molecular Biology
> > Hyderabad 500007
> > I N D I A
> >
> > Fax: (00-91)40-7171195
> > Phone: (00-91)40-7172241
> > -----
> > I love BBSing: All the social dynamics of kindergarten!
> > -----
> > curiouser at ccmb.ap.nic.in
> >
> > ----- Original Message -----
> > From: "Chris Upton" <cupton at uvic.ca>
> > To: <methods at hgmp.mrc.ac.uk>
> > Sent: Thursday, April 05, 2001 5:37 AM
> > Subject: Re: computational analysis of sequences
> >
> > > Check out BLAST Search Updater:  http://athena.bioc.uvic.ca/genomes
> > >
> > > Chris Upton
> > >
> > >
> > > In article <3ACAEB0D.657136BC at bbm1.ucm.es>, Sergio <sergioal at bbm1.ucm.es>
> > wrote:
> > >
> > > > I got a similar problem, and solved it in a not very elegant way.
> > > > The baylor college of medicine offers a batch server to analyze many
> > > sequences,
> > > > but you should install it into your computer and, at least in my case,
> > > it didn't
> > > > work
> > > (http://searchlauncher.bcm.tmc.edu/downloads/software/batch_client.html) .
> > > > So i was almost resigned to send the sequences of my ORFs one by one
> > > (they were
> > > > only fifty, so it was not a big deal) using the web server from the EBI,
> > > > (http://www.ebi.ac.uk/) opening around 10 or 12 navigator windows at a
> > time.
> > > > Finally i found faster, and less resources spending, to send the
> > sequences via
> > > > e-mail to this server, so i wrote a very simple C++ program wich found
> > > the ORFs
> > > > and generates .txt files with the information the server needs (one ORF
> > per
> > > > file), and afterwards i sent the files pasting them in a e-mail template
> > (once
> > > > you get the rhythm with the mouse and Ctr-C Ctr-V you can do it very
> > > fast... but
> > > > everyone will look at you asking what's wrong with you... too much
> > coffee
> > > > maybe?) . If you are more skilled in programming maybe you would prefer
> > > to make
> > > > a program which could send the sequences by its own... and share it
> > ;-).
> > > >
> > > > Sergio
> > > >
> > > > "S.Tiwari" wrote:
> > > >
> > > > > I will be going for random sequencing of my clones from a flower cDNA
> > > > > library from a  weed related to arabidopsis. Once I get the clones
> > > > > sequenced i have to compare the sequences with the arabidopsis
> > database.
> > > > >
> > > > > I would like to know if it is possible to do a blast analysis or
> > > > > anything similar with a batch of sequences otherwise if i have to go
> > for
> > > > > blast with each of my sequence it will take a lot of time and energy.
> > > > >
> > > > > Please help with comment's/suggestions.
> > > > > Thanx!
> > > > > sumis
> > > --
> > > Dept Biochemistry and Microbiology
> > > University of Victoria
> > > Victoria BC
> >
> > ---
> 
> --
> *********************************************
> Sushma Tiwari
> Department of Biology and Biochemistry
> South Building
> University of Bath
> Claverton Down,
> BATH,
> BA2 7AY,
> UK.
> Phone: 01225 826826 ext 5427
> Fax : 01225 826779
> *********************************************
> 
> 

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