[Bioperl-l] NCBI Blast via HTTP

dwaner at scitegic.com dwaner at scitegic.com
Wed Mar 14 12:10:40 EDT 2007


We have seen this too, and I think I have tracked it down to recent 
changes in NCBI's results page format.  Specifically, there is no longer 
the QBlastInfo block that BioPerl uses to detect that the results are 
ready. There is also no closing PRE tag that BioPerl uses to detect the 
end of the blast results text. 

Also, in looking at the BioPerl code, I see that  it is assuming that 
"QBlastInfoBegin" and "Status=READY" are on separate lines. This is not 
always the case, and has caused failures for us in the past.

I am looking into this now, and communicating with NCBI about the format 
changes.   I will keep the BioPerl list updated when I know more.

David Waner
Bioinformatics Software Engineer
Accelrys/SciTegic



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