[Bioperl-l] Blast information

Brian Osborne bosborne11 at verizon.net
Wed Oct 18 13:10:34 EDT 2006


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
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




More information about the Bioperl-l mailing list