[Bioperl-l] Blast information

[Jason Stajich]

I think this will work for you.

The seq_inds method parses the middle homology sequence and  
classifies each alignment column and returns a list of the columns  
meeting the criteria.  You can interrogate query or hit in this case  
since you are requiring it to be identical

my $identicalbases = scalar $hsp->seq_inds('query', 'identical');
my $conservedbases =  scalar $hsp->seq_inds('query','conserved');

Conserved returns those identical or conserved, if you want just  
those with conservative replacements use 'conserved-not-identical'

See http://bioperl.org/wiki/HOWTO:SearchIO#Table_of_Methods for more  
info.

-jason
On Oct 18, 2006, at 8:16 AM, Kevin Brown 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
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich, PhD
Miller Research Fellow
University of California
Dept of Plant and Microbial Biology
321 Koshland Hall #3102
Berkeley, CA 94720-3102
lab: 510.642.8441
http://pmb.berkeley.edu/~taylor/people/js.html