Sequence alignment from BLAST output

Mark Nance via (by mrnance from
Mon Sep 15 14:37:27 EST 2008


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.


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Today's Topics:

   1. RE: Sequence alignment from BLAST output (Jayakumar, R)


Message: 1
Date: Sat, 13 Sep 2008 15:59:09 -0400
From: "Jayakumar, R" <R.Jayakumar from>
Subject: RE: Sequence alignment from BLAST output
To: "ab" <anirbn from>, <methods from>
	<97101976F8A044468CA74FE11883B90E173E7B16 from>
Content-Type: text/plain; charset="us-ascii"

If there is, you should find a link from or, 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.  :-))

-----Original Message-----
From: methods-bounces from
[mailto:methods-bounces from] On Behalf Of ab
Sent: Saturday, September 13, 2008 1:46 AM
To: methods from
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.


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