Kmer-SSR: a fast and exhaustive SSR search algorithm

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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 100% recall and accurately identifies every SSR of any specified length. To identify more biologically pertinent SSRs, we also developed several filters that allow users to easily view a subset of SSRs based on user input. Kmer-SSR, coupled with the filter options, accurately and intuitively identifies SSRs quickly and in a more user-friendly manner than any other SSR identification algorithm.

Availability and implementation:

The source code is freely available on GitHub at https://github.com/ridgelab/Kmer-SSR.

Contact:

perry.ridge@byu.edu

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