[Biopython] Passing sequence to local BLAST

[Peter Cock]

On Thu, Jul 21, 2011 at 4:51 PM, malvika sharan <malvikasharan at gmail.com> wrote:
> Hi,
>
> i have tried this tool for aligning 1 sequence ( 'aseq.fasta ') against 5
> sequence present in other file ('bseq.fasta'). as expected aseq.fasta gives
> pairwise alignment with every fasta sequence present in bseq.fasta.
>
> the alignment works perfectly and saves the alignment output as well.
>
> 1> the question is if there is anyway to extraxt consensus out of all
> pairwise alignments? I know its is possible with clustalw or muscle or other
> alignment tool. but i do not want pairwise alignment between all the
> sequence with each other. In this case Emboss seemed the better tool where i
> can align all sequence only with 1 query. but the crucial part is to extract
> the conserved residue from the alignment.
>
> 2> The best would be to align all the sequence together against 1 sequence
> (aseq.fasta) like it happens in COBALT. and find the conserved residue
> directly. but i did not find any commandline tool like that unfortunately.
> It would be great if you can suggest a tool if you know any.
>
> thank you !
> Malvika

I don't understand what you are asking for - it is hard to define a
consensus from a pairwise alignment. Could you give a short example?

Also this thread really is going off topic, perhaps a new email thread
(with a more relevant title) would be better?

Peter