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Open Access Technical Note

New finite-size correction for local alignment score distributions

Yonil Park, Sergey Sheetlin, Ning Ma, Thomas L Madden and John L Spouge*

Author Affiliations

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA

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BMC Research Notes 2012, 5:286  doi:10.1186/1756-0500-5-286

Published: 12 June 2012



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.


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.


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 ( webcite).