[Bioperl-l] Modifying Blast plus parameters

[Paul Cantalupo]

Hi Oz,

SInce BLAST is a local alignment tool, perhaps you want something like
Needle http://www.ebi.ac.uk/Tools/psa/emboss_needle/nucleotide.html which
performs a global alignment?

You can add the '-perc_identity' option to the blastn command line like so:
   blastn -perc_identity 80

to limit results to >=80% identity.

Paul


Paul Cantalupo
University of Pittsburgh


On Tue, Apr 29, 2014 at 12:49 PM, Oz <oz.sharabi at mail.huji.ac.il> wrote:

> Hi Paul,
> Thank you for your quick and informative reply.
> Yes, it is a local blast. About sequence coverage - I meant that I do not
> want the algorithm to split the query to two sub-sequences (or more) and
> then align each one at different location. Just to align it as one
> continous sequence.
> Also, I would like to make these restrictions during the Blastplus running
> and not to screen the un-wanted results afterwards..
> Since I'm a "green" user, could you please specify where I add the
> -perc_identity (I couldn't find example on the web)?
> Thank you very much,
> Oz
>
>
>
>
> --
> View this message in context:
> http://bioperl.996286.n3.nabble.com/Modifying-Blast-plus-parameters-tp17461p17478.html
> Sent from the Bioperl-L mailing list archive at Nabble.com.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>