New finite-size correction for local alignment score distributions.
BACKGROUND
Local alignment programs often calculate the probability that a match occurred by chance. The calculation of this probability may require a "finite-size" correction to the lengths of the sequences, as an alignment that starts near the end of either sequence may run out of sequence before achieving a significant score.


RESULTS
We present an improved finite-size correction that considers the distribution of sequence lengths rather than simply the corresponding means. This approach improves sensitivity and avoids substituting an ad hoc length for short sequences that can underestimate the significance of a match. We use a test set derived from ASTRAL to show improved ROC scores, especially for shorter sequences.


CONCLUSIONS
The new finite-size correction improves the calculation of probabilities for a local alignment. It is now used in the BLAST+ package and at the NCBI BLAST web site ( http://blast.ncbi.nlm.nih.gov).
National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.
Yonil
Y
Park
Sergey
S
Sheetlin
Ning
N
Ma
Thomas L
TL
Madden
John L
JL
Spouge
D000595:Amino Acid Sequence; D030562:Databases, Protein; D020407:Internet; D008969:Molecular Sequence Data; D011336:Probability; D012107:Research Design; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data; D012984:Software