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jasonsahl / LS-BSR

Large scale Blast Score Ratio (BSR) analysis
GNU General Public License v3.0
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ls-bsr > 1 #13

Closed maesaar closed 8 years ago

maesaar commented 8 years ago

Dear Jason Sahl, I used ls-bsr with nucleotide data using blastn and got bsr values higher than 1.

Then I used same dataset but protein data with blast separately (not with ls-bsr) with blastp and still got few BSRs higher than 1.

Could you explain why is that or what could I do to avoid BSR values higher than 1 ?

Thanks?

jasonsahl commented 8 years ago

Can you confirm that you are using the most recent version of the source code? If so, would it be possible to email me one coding region and one genome where you observed this? thanks,

maesaar commented 8 years ago

Yes it is latest version! I uploaded files:

https://drive.google.com/open?id=0B4WodULrYQM_TXNiZkJsaVMtWU0

jasonsahl commented 8 years ago

Thanks for the files. The problem is the gaps that are in your nucleotide files. When I remove those, the BSR values drop to <=1. Stand alone blast also throws this error:

CFastaReader: Hyphens are invalid and will be ignored around line 3

If you need to keep them in, try using BLAT for alignments. In my test of your file, it didn't seem to care.

Jason