[Bioperl-l] Blast information

Kevin Brown Kevin.M.Brown at asu.edu
Wed Oct 18 11:16:50 EDT 2006


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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