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
I hope that will help you
On 28 Jan 2003 09:28:24 -0000, Rudi.Effe at gmx.de (Rudi Effe) wrote:
>>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