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cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly.

Authors :
Lewis TE
Sillitoe I
Lees JG
Source :
Bioinformatics (Oxford, England) [Bioinformatics] 2019 May 15; Vol. 35 (10), pp. 1766-1767.
Publication Year :
2019

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.<br />Results: We present cath-resolve-hits (CRH), a new tool that uses a dynamic-programming algorithm implemented in open-source C++ to handle large datasets 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 datasets.<br />Availability and Implementation: CRH is available at https://github.com/UCLOrengoGroup/cath-tools; documentation is available at http://cath-tools.readthedocs.io.<br />Supplementary Information: Supplementary data are available at Bioinformatics online.<br /> (© The Author(s) 2018. Published by Oxford University Press.)

Details

Language :
English
ISSN :
1367-4811
Volume :
35
Issue :
10
Database :
MEDLINE
Journal :
Bioinformatics (Oxford, England)
Publication Type :
Academic Journal
Accession number :
30295745
Full Text :
https://doi.org/10.1093/bioinformatics/bty863