[Bioperl-l] allowgaps parameter in Bio::SearchIO

Daniel Lang Daniel.Lang at biologie.uni-freiburg.de
Fri Oct 31 08:54:24 EST 2003


Hi,
I´m getting wrong values for the "allowgaps" parameter while parsing
NCBI-like BLAST results:
The parser does not detect if a the report was generated with -g F
switch(ungapped) and the allowgaps values is "yes", when it should be
"no"...
I guess the parameter is based on the occurence of "Gapped" after the
"Lambda"-part, right?

Here is an example BLAST output snipplet(-g F):

Searching..................................................done

  ***** No hits found ******

   Database: ppp_orfpep
     Posted date:  Sep 18, 2003  6:31 AM
   Number of letters in database: 2,367,445
   Number of sequences in database:  14,583

Lambda     K      H
    0.318    0.135    0.401


Matrix: BLOSUM62
Number of Hits to DB: 378,425

Or did I missinterpret the parameter?
Thanks ind advance,
Daniel:)




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