Local alignment of two-base encoded DNA sequence |
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| Authors: | Nils Homer Barry Merriman Stanley F Nelson |
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| Institution: | (1) Department of Computer Science, University of California Los Angeles, Los Angeles, California 90095, USA;(2) Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA |
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| Abstract: | Background DNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA
sequencing technologies do not directly measure the base sequence, but rather an encoded form, such as the two-base encoding
considered here. In order to compare such data to a reference sequence, the data must be decoded into sequence. The decoding
is deterministic, but the possibility of measurement errors requires searching among all possible error modes and resulting
alignments to achieve an optimal balance of fewer errors versus greater sequence similarity. |
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