Journal
BIOINFORMATICS
Volume 24, Issue 13, Pages 1530-1531Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btn223
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Funding
- Max-Planck Society
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We present a tool suited for searching for many short nucleotide sequences in large databases, allowing for a predefined number of gaps and mismatches. The commandline-driven program implements a non-deterministic automata matching algorithm on a keyword tree of the search strings. Both queries with and without ambiguity codes can be searched. Search time is short for perfect matches, and retrieval time rises exponentially with the number of edits allowed.
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