[BiO BB] Re: Is it possible to Blast against genBank files

Peter Groenen peter.groenen at home.nl
Sat Dec 20 07:38:55 EST 2003

It seems that SRS (sequence retrieval system) is still not very well known on the other side of the Atlantic. ;-)
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).
SRS does it all and you can even install Blast, ClustalW within SRS if you're a little more experienced.
Have a look at  srs.ebi.ac.uk
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.
  ----- Original Message ----- 
  From: bio_bulletin_board-request at bioinformatics.org 
  To: bio_bulletin_board at bioinformatics.org 
  Sent: Friday, December 19, 2003 6:01 PM
  Subject: BiO_Bulletin_Board digest, Vol 1 #590 - 3 msgs

  Date: Thu, 18 Dec 2003 12:53:51 -0800 (PST)
  From: jordan swanson <jordanmswanson at yahoo.com>
  Subject: Re: [BiO BB] Is it possible to Blast against genBank files
  To: bio_bulletin_board at bioinformatics.org
  Reply-To: bio_bulletin_board at bioinformatics.org

  > You mean that the BLAST results only have the Fasta
  > file annotation in 
  > them. Well, AFAIK, the only input to formatdb is
  > Fasta or ASN.1. The 
  > output, anyhow, would be a one-liner.
  > How about giving her the output in HTML (-T option)?
  > blast automatically 
  > builds a link from each hit to the NCBI page. So
  > using a browser, your 
  > coworker can skim the one-line annotation, and then
  > click & delve into 
  > the more interesting ones.

  We did try that, however with the large number of
  sequences she needed to look up, she was black-listed
  from their machine.  We need to find the full GenBank
  entry given a particular identifier, unfortunately the
  easiest way I've found so far seems to be the Entrez
  system, and that appears to not be possible to
  download.  Is there another way to get the full
  genbank entry given the identifier?

  Jordan Swanson


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