[Biopython] Passing sequence to local BLAST

[malvika sharan]

yup sure!!

On Thu, Jul 21, 2011 at 6:09 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> 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
>