[Bioperl-l] Re: bug #949

[Roger Hall]

> The current behavior was that the frame sign (+/-) was dependent on the
> query strand.  I don't think it is.

The frame sign is directly parsed from the blast report. It is compared to
the subject strand. The query strand has no direct relationship to either of
those (as far as BPLite, Sbjct, HSP, and Similarity are concerned - not
biologically speaking) - and no relationship to the error msg.



And wait just a sec on the second HSP for the first subject:

> But for the next HSP of the same Sbjct
>  Score =  156 bits (391), Expect = 3e-37
>  Identities = 76/97 (78%), Positives = 83/97 (85%)
>  Frame = +3
>
> Query: 2706 GRARWLTPVIPALWDAKVGISSEVRSSRPAWPTWQNSVFMKNTKISQAWWQAPVIPANWE
2885
>             GRARWLTPVIPALW+A+ G S EVRSSRPAWPTW N V  KNTKIS+AWW+APVIPA  E
> Sbjct: 1    GRARWLTPVIPALWEAEAGGSPEVRSSRPAWPTWXNPVSTKNTKISRAWWRAPVIPATRE
60
>
> Query: 2886 AEAGESLESRRQRLQ*AEIVPLHSSLGDKSKTLSQKK 2996
>             AEAGESLE  R+RLQ AEI PLHSSLG+KS+T SQKK
> Sbjct: 61   AEAGESLEPGRRRLQXAEIAPLHSSLGNKSETPSQKK 97

Actual Query START= 2706
Actual Query END = 2996

when Actual Query START < END  ->  query strand = 1 (! -1): so says
HSP::new()

> query start = 2706
> query end   = 2996
> query strand= -1
>
> sbjct start = 1
> sbjct end   = 97
> sbjct strand= 1
>
> Frame = +3
>

+1 ~ +3 : No warning is generated for this HSP because the subject strand is
also positive. HSP warnings are given for the HSP's 1 and 3 (plus more).

Please verify!

Thanks!

Roger