Sequence alignment from BLAST output

ab via methods%40net.bio.net (by anirbn from gmail.com)
Wed Sep 17 00:41:42 EST 2008


Thanks a ton Mark. That was quite helpful.

Best,

Anirban.


On Sep 15, 3:37 pm, "Mark Nance" <mrna... from lsi.umich.edu> wrote:
> Anirban,
>
> You can use the protein blast from pubmed.  After your blast, scroll down and check the boxes next to the sequences you want.  Click the "Get Selected Sequences" box.  On the Results page it sends you to, pull down the Display option to get FASTA.  Pull down the Send To option, and choose text.  You can then copy/paste all of the sequences you selected into ClustalW.  You still have to copy and paste, but you only have to do it once.
>
> Mark
>
> >>> <methods-requ... from oat.bio.indiana.edu> 09/14/08 1:04 PM >>>
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>    1. RE: Sequence alignment from BLAST output (Jayakumar, R)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 13 Sep 2008 15:59:09 -0400
> From: "Jayakumar, R" <R.Jayaku... from roswellpark.org>
> Subject: RE: Sequence alignment from BLAST output
> To: "ab" <ani... from gmail.com>, <meth... from magpie.bio.indiana.edu>
> Message-ID:
>         <97101976F8A044468CA74FE11883B90E173E7... from VISTA.roswellpark.org>
> Content-Type: text/plain; charset="us-ascii"
>
> If there is, you should find a link fromwww.expasy.chorwww.bioinformatik.de, two of the largest repositories of molecular tools
> on the web.  But I wish there were tools which will do all our work
> while we relax with a martini in front of the fireplace, but
> unfortunately, some amount of work is required.  :-))
> Jay
>
> -----Original Message-----
> From: methods-boun... from oat.bio.indiana.edu
>
> [mailto:methods-boun... from oat.bio.indiana.edu] On Behalf Of ab
> Sent: Saturday, September 13, 2008 1:46 AM
> To: meth... from magpie.bio.indiana.edu
> Subject: Sequence alignment from BLAST output
>
> Dear all,
>
> Sorry about the silly question. Is there any website where one can BLAST
> microbial genomes with a protein sequence, select a subset from the
> BLAST output and make a multiple sequence alignment (with CLUSTAL_W or
> equivalent) without the need to individually copy/paste every selected
> sequence into a separate file ?
>
> Thanks very much in advance.
>
> Best,
>
> Anirban.
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