[Biodevelopers] forcing a full sequence comparison in blast

[Martin Gollery]

Hi Phil,
It sounds like you want a Global search, not a local one like BLAST.
Try 'Needle' from the EMBOSS package- I think that may work for you.

Marty

On 4/9/07, Phil Princely <phil.princely at gmail.com> wrote:
> Hi all,
>
> I'm working on a script to compare all genes in a genome against a
> full sequence in a blast database. both have around 2000 genes. my
> script takes the test genome, extracts one amino acid sequence and
> runs it through blast. it then filters the output to grab only the
> name of the gene with the best match and the similarity (in percent).
> For example, from these lines:
>
> >Contig 165-147: 171558..172979 (reverse), 474 amino acids
>  Identities = 471/473 (99%), Positives = 471/473 (99%)
>
> it grabs the text Contig 165-147 and the percent 99%.
>
> My problem comes when sequences have a lower similarity, and blast
> uses only a section of the input gene. For example
>
> >Contig 158-62: 61482..62750 (direct), 423 amino acids
>  Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
>
> Here, it's only used 46 of the amino acids, where the full gene
> sequence has 347.
>
> Is there a way I can force blast to use the full 347 amino acids for
> comparison. The researchers in my lab are most interested in places
> with low similarities, since they are trying to find the portions
> which make this organism virulent.
>
> Thanks again
>
> Phil P.
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-- 
-- 
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS334
775-784-7042
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