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cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly.
- 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.)
- Subjects :
- Algorithms
Documentation
Proteins
Software
Subjects
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