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

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 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 benchmar

SUBMITTER: Lewis TE 

PROVIDER: S-EPMC6513158 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature