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<DIV><FONT face=Arial size=2>It seems that SRS (sequence retrieval system) is
still not very well known on the other side of the Atlantic. ;-)</FONT></DIV>
<DIV><FONT face=Arial size=2>It is for free (up to version 7 I believe, for
Academic users) and is still one of the best solutions for these things (instead
of starting to hack around with Perl again).</FONT></DIV>
<DIV><FONT face=Arial size=2>SRS does it all and you can even install
Blast, ClustalW within SRS if you're a little more
experienced.</FONT></DIV>
<DIV><FONT face=Arial size=2>Have a look at <A
href="http://srs.ebi.ac.uk">srs.ebi.ac.uk</A></FONT></DIV>
<DIV><FONT face=Arial size=2>You'll find some more related stuff ad you can
download all info and binaries from their FTP site. Be aware thta you'll need a
little experience to administrate the application. But you'll succeed pretty
quick.</FONT></DIV>
<BLOCKQUOTE
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=bio_bulletin_board-request@bioinformatics.org
href="mailto:bio_bulletin_board-request@bioinformatics.org">bio_bulletin_board-request@bioinformatics.org</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A
title=bio_bulletin_board@bioinformatics.org
href="mailto:bio_bulletin_board@bioinformatics.org">bio_bulletin_board@bioinformatics.org</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Friday, December 19, 2003 6:01
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> BiO_Bulletin_Board digest, Vol 1
#590 - 3 msgs</DIV><BR>Date: Thu, 18 Dec 2003 12:53:51 -0800 (PST)<BR>From:
jordan swanson <<A
href="mailto:jordanmswanson@yahoo.com">jordanmswanson@yahoo.com</A>><BR>Subject:
Re: [BiO BB] Is it possible to Blast against genBank files<BR>To: <A
href="mailto:bio_bulletin_board@bioinformatics.org">bio_bulletin_board@bioinformatics.org</A><BR>Reply-To:
<A
href="mailto:bio_bulletin_board@bioinformatics.org">bio_bulletin_board@bioinformatics.org</A><BR><BR>>
You mean that the BLAST results only have the Fasta<BR>> file annotation in
<BR>> them. Well, AFAIK, the only input to formatdb is<BR>> Fasta or
ASN.1. The <BR>> output, anyhow, would be a one-liner.<BR>> <BR>> How
about giving her the output in HTML (-T option)?<BR>> blast automatically
<BR>> builds a link from each hit to the NCBI page. So<BR>> using a
browser, your <BR>> coworker can skim the one-line annotation, and
then<BR>> click & delve into <BR>> the more interesting
ones.<BR><BR>We did try that, however with the large number of<BR>sequences
she needed to look up, she was black-listed<BR>from their machine. We
need to find the full GenBank<BR>entry given a particular identifier,
unfortunately the<BR>easiest way I've found so far seems to be the
Entrez<BR>system, and that appears to not be possible to<BR>download. Is
there another way to get the full<BR>genbank entry given the
identifier?<BR><BR>---<BR>Jordan
Swanson<BR><BR>__________________________________<BR></BLOCKQUOTE></BODY></HTML>