Nov 12, 2015

Are all global alignment algorithms and implementations correct?

BioRxiv : the Preprint Server for Biology
Tomáš FlouriAlexandros Stamatakis

Abstract

While implementing the algorithm, we discovered two mathematical mistakes in Gotoh's paper that induce sub-optimal sequence alignments. First, there are minor indexing mistakes in the dynamic programming algorithm which become apparent immediately when implementing the procedure. Hence, we report on these for the sake of completeness. Second, there is a more profound problem with the dynamic programming matrix initialization. This initialization issue can easily be missed and find its way into actual implementations. This error is also present in standard text books. Namely, the widely used books by Gusfield and Waterman. To obtain an initial estimate of the extent to which this error has been propagated, we scrutinized freely available undergraduate lecture slides. We found that 8 out of 31 lecture slides contained the mistake, while 16 out of 31 simply omit parts of the initialization, thus giving an incomplete description of the algorithm. Finally, by inspecting ten source codes and running respective tests, we found that five implementations were incorrect. Note that, not all bugs we identified are due to the mistake in Gotoh's paper. Three implementations rely on additional constraints that limit generality. Thus, only two...Continue Reading

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Mentioned in this Paper

Awareness
Extracellular Matrix
Phylogenetic Analysis
Medical Devices
Bio-Informatics
Description
Analysis
Developmental Arithmetic Disorder
Nepomorpha
Sequence Alignment

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