It sounds as though you want to do a multiple alignment, using software such
as CLUSTALW, and avoid BLAST entirely for this project.
If this doesn't meet your needs, you can consider writing your own software
which manipulates BLAST results. E.g., you can use BioPerl
(www.bioperl.org) as a building block to write your software, since it knows
how to parse BLAST output and also has well-defined notions of DNA sequence
data and its manipulation.
"Rudi Effe" <Rudi.Effe at gmx.de> wrote in message
news:kg633vcpp889amhb4d6sb6n8l57lhhcpoc at 4ax.com...
> 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?
>> Thank you for any hint!