Kmer-SSR: a fast and exhaustive SSR search algorithm.

ABSTRACT:

Motivation

One of the main challenges with bioinformatics software is that the size and complexity of datasets necessitate trading speed for accuracy, or completeness. To combat this problem of computational complexity, a plethora of heuristic algorithms have arisen that report a 'good enough' solution to biological questions. However, in instances such as Simple Sequence Repeats (SSRs), a 'good enough' solution may not accurately portray results in population genetics, phylogenetics and forensics, which require accurate SSRs to calculate intra- and inter-species interactions.

Results

We present Kmer-SSR, which finds all SSRs faster than most heuristic SSR identification algorithms in a parallelized, easy-to-use manner. The exhaustive Kmer-SSR option has 100% precision and 1

SUBMITTER: Pickett BD 

PROVIDER: S-EPMC5860095 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature