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Two Cases of Data Overflow in the Protein Sequencing Program BLASTPGP

Kristoffer Osowski, Jan Westerholm, Mats Aspnäs, Two Cases of Data Overflow in the Protein Sequencing Program BLASTPGP. TUCS Technical Reports 813, Turku Centre for Computer Science, 2007.

Abstract:

For some input sequences, the NCBI BLASTPGP program for gapped basic local alignment search
fails, because of errors in the program implementation. One error causes the blastpgp program
to crash for certain input sequences, failing to produce any valid results. An other error causes a
large number of warning messages <I>ObjMgrNextAvailEntityID failed with idx 2048</I> to be
output, and the program produces incorrect and incomplete search results. This report describes
our investigation of the causes of these errors and a correction to both errors.

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BibTeX entry:

@TECHREPORT{tOsWeAs07a,
  title = {Two Cases of Data Overflow in the Protein Sequencing Program BLASTPGP},
  author = {Osowski, Kristoffer and Westerholm, Jan and Aspnäs, Mats},
  number = {813},
  series = {TUCS Technical Reports},
  publisher = {Turku Centre for Computer Science},
  year = {2007},
  keywords = {BLAST, BLASTPGP},
  ISBN = {978-952-12-1891-0},
}

Belongs to TUCS Research Unit(s): High Performance Computing and Communication

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