extracting domain from a BLAST search

Francis Durst francis.durst at bota-ulpnospam.u-strasbg.fr
Wed May 17 12:47:29 EST 2000

In article <39216873.FC42603D at sb-roscoff.fr> crepinau at sb-roscoff.fr (=?iso-8859-1?Q?Cr=E9pineau?= Florent) writes:
>From: crepinau at sb-roscoff.fr (=?iso-8859-1?Q?Cr=E9pineau?= Florent)
>Subject: extracting domain from a BLAST search
>Date: 16 May 2000 16:24:18 +0100

>    hello,

>I am looking for a software like clustering from X. Guan that would take
>a Blast output (idealy a Psi Blast output) to identify and extract
>domains. Or which would take a multiple alignement output and generate
>domains. Or which would take a set of protein sharing a domain and would
>find and extract that domain.

>Do you know of anyting like this ?

>Thank you for reading my message.


You can use the pgm at http://blocks.fhcrc.org/blocks/process_blocks.html to 
get blocks from any alignment in fasta or clustal format. (This is part of 
designing degenerated primers with Codehop).

All the best


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