[Bioperl-l] not recognizing hsp in a hit
Dave Messina
David.Messina at sbc.su.se
Thu Apr 7 09:02:26 UTC 2011
Hi Cynthia,
Please remember to reply all so this discussion stays on the list.
It may very well be a problem with the blat parser so please submit:
- your blat output
- your script
- the output from your script
to our bug tracker.
The reason we need your script is that it will allow us to confirm what you're seeing. More importantly, in order to fix problems like this, we need a test case, and your code will form the basis for that. So it would be a big help for us.
Thanks!
Dave
On Apr 6, 2011, at 18:36, Cynthia Lee Page <Cynthia.Page at Colorado.EDU> wrote:
> HI Dave -
>
> I was talking to my boss about this and a couple things she pointed out to me: first this is a blast report but I actually ran blat on two closely related organisms and used the option blat -out = blast. So in reality this is not an actual blast report and it is my understanding that due to the fact reporting of hsp can be effected as follows, when hsp's are on the same chromosome it will report them as separate hits.
>
> This is what happen in both cases I presented. In YCL068C, 3 hits, 3 hsp and all are on Chr3. In the case of YCL067C 3 hits were reported and no hsp which is the curious part. In both cases the two highest hsp were roughly the same distance apart on the chromosome the highest around 200,000 and the second around 15,000.
>
> Perhaps this is sufficiently far apart on the chromosome for situation the my boss was referring to. I still have the problem however of not having the hsp's recognized. So I will proceed by just blatting that gene against the query and see if the report changes. If not, hmm.
>
> I am a newbie with perl so it certainly could be a problem with the script, but since other genes are parsing as expected it is more likely that the problem is due to the nature of the blat report. In the next few days I will redo the blat on that gene alone and let you know what happen, if you would like.
>
> Any comments you may have are welcome
>
>
> Thanks a lot,
>
> Cynthia
>
> On Apr 6, 2011, at 7:57 AM, Dave Messina wrote:
>
>> 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.
>>
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