[Biopython] Hello

[Joao Mamede]

Hello,
Well, I think I solved my problem.
I just run blast locally and identified the regions where each small 
sequence, around 75nt, aligns into the hit sequence that was identified 
from soap.
By the way anyone has a small code to use blastn with the "vector" 
database to remove possible vector DNA?

Thanks
João


Brad Chapman wrote:
> 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
>