PSimScan: algorithm and utility for fast protein similarity search.

ABSTRACT: In the era of metagenomics and diagnostics sequencing, the importance of protein comparison methods of boosted performance cannot be overstated. Here we present PSimScan (Protein Similarity Scanner), a flexible open source protein similarity search tool which provides a significant gain in speed compared to BLASTP at the price of controlled sensitivity loss. The PSimScan algorithm introduces a number of novel performance optimization methods that can be further used by the community to improve the speed and lower hardware requirements of bioinformatics software. The optimization starts at the lookup table construction, then the initial lookup table-based hits are passed through a pipeline of filtering and aggregation routines of increasing computational complexity. The first step in this p

SUBMITTER: Kaznadzey A 

PROVIDER: S-EPMC3591303 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature