[Biodevelopers] forcing a full sequence comparison in blast

minky ARORA minky81 at gmail.com
Wed Apr 11 10:01:05 EDT 2007


How about if you turn the filter off using the -F F option? DOing this
should give u exact matches.

On 4/6/07, 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.
> _______________________________________________
> Biodevelopers mailing list
> Biodevelopers at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biodevelopers
>


More information about the Biodevelopers mailing list