Lewis, TE;
Sillitoe, I;
Lees, JG;
(2018)
cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly.
Bioinformatics
, 35
(10)
pp. 1766-1767.
10.1093/bioinformatics/bty863.
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Abstract
MOTIVATION: Many bioinformatics areas require us to assign domain matches onto stretches of a query protein. Starting with a set of candidate matches, we want to identify the optimal subset that has limited/no overlap between matches. This may be further complicated by discontinuous domains in the input data. Existing tools are increasingly facing very large data-sets for which they require prohibitive amounts of CPU-time and memory. RESULTS: We present cath-resolve-hits (CRH), a new tool that uses a dynamic-programming algorithm implemented in open-source C ++ to handle large data-sets quickly (up to ∼1 million hits/second) and in reasonable amounts of memory. It accepts multiple input formats and provides its output in plain text, JSON or graphical HTML. We describe a benchmark against an existing algorithm, which shows CRH delivers very similar or slightly improved results and very much improved CPU/memory performance on large data-sets. AVAILABILITY AND IMPLEMENTATION: CRH is available at https://github.com/UCLOrengoGroup/cath-tools; documentation is available at http://cath-tools.readthedocs.io.
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