[Bioperl-l] not recognizing hsp in a hit

[Dave Messina]

Hi Cynthia,

Hmm, curious.

Thanks for including your script's output and parts of the blast reports. I
would like to see more if I could, though. Would you please go ahead and
include your script and the complete blast reports for those two genes? If
the files are too big to attach to email, then you can create a bug report
and attach the files to that.

Instructions are here:
http://www.bioperl.org/wiki/Bugs


Dave





On Tue, Apr 5, 2011 at 19:50, pageski <Cynthia.Page at colorado.edu> wrote:

>
> Hi I am new to this forum so please forgive me if I make faux pas!
>
> I am parsing a BLAST report using bioperl for some reason one of my hits
> which list three hsp is not recognizing them as hsp and during the parsing
> they are getting skipped over. I have print to screen output showing two
> genes the first is the one I am referring to and the second is one that is
> working just for your comparison. I will also paste part of the BLAST
> report
> for those two entries.
>
> I will not paste the code at this time, but will gladly if it is needed. I
> am thinking that perhaps I am misunderstanding what an hsp is ... that is
> why I am first showing you these two pieces of informations.
>
> Thanks for any help!
> ##############################################################
> I have pasted screen output from my script I use to trouble shoot plus part
> of
> a BLAT output in Blast format. From the BLAST output you can see I have
> three hits on Chr3
> it seems to me that this should be three hsp's however these are not
> considered hsp for some reason
> yet YCL068 is - I pasted part of that report below YCL067
>
> ############screen output##########################################
> YCL067C
> C
> 3
> chr3
> This is the number of hsps: 0 for YCL067C
> Number of hsp == :0 for  YCL067C
> This is the hitscore: 1222 for name: YCL067C
>  This is the highesthit score: 1222 for Name: YCL067C
> YCL067C
>
>
> YCL068C
> C
> 3
> chr3
> This is the number of hsps: 3 for YCL068C
> This is the number of hsps:3 for name: YCL068C
>  I am in the if hsps >0 and evaluating YCL068C
> This is the number of hits:3 for name: YCL068C
> This is the hitscore: 1508 for name: YCL068C
>  This is the highesthit score: 1508 for Name: YCL068C
>  This is the percent of hsp percentid:99.6173469387755
> ######################################################
>
> ###################Part of Blast report for YCL067C################
>
>
> Query= YCL067C
>         (633 letters)
>
> Database: /data/genomes/Sigma1278b/sigmav7.fa
>           16 sequences; 11,945,947 total letters
>
> Searching.done
>                                                                 Score    E
> Sequences producing significant alignments:                      (bits)
> Value
>
> chr3                                                                 1222
> 0.0
> chr3                                                                 1222
> 0.0
> chr3                                                                 1078
> 0.0
>
>
>
> >chr3
>          Length = 319572
>
>  Score = 1222 bits (3153), Expect = 0.0
>  Identities = 633/633 (100%)
>  Strand = Minus / Plus
> ############################################
> Query= YCL068C
>         (783 letters)
>
> Database: /data/genomes/Sigma1278b/sigmav7.fa
>           16 sequences; 11,945,947 total letters
>
> Searching.done
>                                                                 Score    E
> Sequences producing significant alignments:                      (bits)
> Value
>
> chr3                                                                 1508
> 0.0
> chr3                                                                 1505
> 0.0
> chr3                                                                   91
> 1e-18
>
>
>
> >chr3
>          Length = 319572
>
>  Score = 1508 bits (3891), Expect = 0.0
>  Identities = 781/784 (100%)
>  Strand = Minus / Plus
>
> --
> View this message in context:
> http://old.nabble.com/not-recognizing-hsp-in-a-hit-tp31326619p31326619.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>