[Biopython] Hello

[Brad Chapman]

João;

> So, my problem. I have a set of sequences I want to assemble, using the
> sequence of the gene that soap recognized as the "reference".
> I am able to to this manually in seconds for each gene with a closed
> source program called "Geneious".
> However: I wanted to do this automatically from python. I tried abyss
> TIGR-assembler(and others) with not much sucess I must say.
> I also tried to align with the traditional "clustal and muscle" but it
> takes forever and of course I don't have enough RAM.
> What I need is to output the location of each small sequence within a
> ENtrez sequence .
> Is local blast an option?Analysing each small sequence against a small
> db?(I will not have a real assembly like this).

It is not totally clear to me exactly what your input and goals are.
Are you dealing with next gen short reads, from Illumina or 454? If
so, your best bet is to use a short read aligner to place them on
the reference sequences. Then use a downstream SNP calling/coverage or
assembly program depending on your needs.

Above you mentioned SOAP; are you referring to:

http://soap.genomics.org.cn/

If so, then there are integrated programs there that should help
with your downstream analysis. If you are re-sequencing for SNPs,
then SOAPsnp is the program to look at. If you are assembling
contigs from scratch, try SOAPdenovo.

Hope this helps,
Brad