Or ggsearch or ssearch in fasta package
On Mon, May 5, 2014 at 5:58 AM, 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
> performs a global alignment?
> You can add the '-perc_identity' option to the blastn command line like
> blastn -perc_identity 80
> to limit results to >=80% identity.
> Paul Cantalupo
> University of Pittsburgh
> On Tue, Apr 29, 2014 at 12:49 PM, Oz 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
> > want the algorithm to split the query to two sub-sequences (or more)
> > 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
> > 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
> > --
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