[Bioperl-l] Blast information

Kevin Brown Kevin.M.Brown at asu.edu
Wed Oct 18 17:25:48 EDT 2006


Yes, that does indeed look like what I was after. 

> -----Original Message-----
> From: Brian Osborne [mailto:bosborne11 at verizon.net] 
> Sent: Wednesday, October 18, 2006 10:11 AM
> To: Kevin Brown; bioperl-l
> Subject: Re: [Bioperl-l] Blast information
> 
> Kevin,
> 
> Are you looking for hsp_length()? See the SearchIO HOWTO for a list of
> methods:
> 
> http://www.bioperl.org/wiki/HOWTO:SearchIO
> 
> 
> Brian O.
> 
> 
> On 10/18/06 11:16 AM, "Kevin Brown" <Kevin.M.Brown at asu.edu> wrote:
> 
> > I just recently upgraded to 1.5.1 on WinXP to bring this 
> version closer
> > to live to parse some locally created blast files.  I'm 
> trying to find
> > the method that returns the values that are underneath the 
> Identities
> > and Positives information as I'm trying to replicate the 
> output of an
> > old blast parser we have here written in RealBasic which is 
> showing its
> > age.  Once I have it replicating the old output I then intend to add
> > more features in terms of filtering returned hits (like not 
> returning
> > self->self hits or a->b so don't show b->a).
> > 
> > Example:
> > I'm looking for the methods that will return 117 from 
> identities and 117
> > from positives.  I can't just use 
> num_identical/percent_identity as that
> > isn't 100% accurate.
> > 
> >> BurkM_2016
> >           Length = 241
> > 
> >  Score = 43.2 bits (88), Expect = 7e-005
> >  Identities = 26/117 (22%), Positives = 51/117 (43%)
> > 
> > Query: 298 
> QEEFFYAFEALVANKAQVIITSDTYPKEISGIDDRLISRFDSGLTVAIEPPELEMRVAIL
> > 357
> >            Q   F  F  + A+    ++ +         + + L +R   GL   + 
> P   E + A+L
> > Sbjct: 111 
> QIALFNLFNEVRAHPMTALVVAGPAAPLALDVREDLRTRLGWGLVFHLAPLTDEGKAAVL
> > 170
> > 
> > Query: 358 
> MRKAQSEGVSLSEDVAFFVAKHLRSNVRELEGALRKILAYSKFHGREITIELTKEAL 414
> >               A+  G++L++DV  ++  H R ++  L   L  +  +S    R +T+ L +  L
> > Sbjct: 171 
> KHAAKERGIALADDVPSYLLTHFRRDMPSLMSLLDALDRFSLEQKRAVTLPLLRAML 227
> > 
> > Thanks,
> > Kevin
> > 
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 



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