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BLAST software?

Olivier Friard olivier.dot.friard.at.laposte.dot.net at host.free.fr
Fri Jan 31 08:52:02 EST 2003


Hi,
try to:

1) extract sequences from your BLAST output (or FASTA output) with the
FASTA-BLAST_scan program (http://annhyb.free.fr)
2) do a multi-alignment with all extracted sequences using CLUSTALW
3) "clean" the CLUSTALW output with the multi-alignment cleaner tool
from AnnHyb (http://annhyb.free.fr)
You will obtain a result like this:

ref. seq.  CATGCTAGCTAGTACCGC
seq.#1     ......T...........
seq.#2     ..........C.......


I hope that will help you
bye
Olivier Friard




On 28 Jan 2003 09:28:24 -0000, Rudi.Effe at gmx.de (Rudi Effe) wrote:

>Hi there,
>
>I am doing research on mutations of a Bacteria. Using BLAST on the web,
>I get alignments like
>
>Query:  21 TGCTGT...
>           || | |...
>Orig.: 321 TGGT-T...
>
>where 98% are identical (600+ positions).
>
>I need a survey, which sample query mutates at what positions. So far I
>seem to must check manually: Write down the positions for each query and
>so on. Is there no way to do a multiple compare? Or even create the
>table of differences automatically?

olivier dot friard at laposte dot net





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