A parallel peptide indexer and decoy generator for crux tide using OpenMP

Target-Decoy database is a common dependable strategy used in Peptide-Spectrum-Matching (PSM) for quality assessment. In this, a set of decoy labeled peptides are injected to the database and indexed along with real peptides. Crux Tide is a fast search engine that supports indexing peptides' database and decoys generation. In Tide, indexing FASTA files and generating decoys is a computationally expensive process. In this paper we first analyze the serial Tide indexer and decoy generator algorithm and, then describe a parallel shared memory solution. Our proposed technique utilizes a clever hashing technique to localize the process, and breaks up the processing dependency among threads. The developed parallel versions are able to reduce the computational complexity by approximately 50% and 25% of the sequential time using 4 and 8 threads, respectively. Moreover, our proposed solution could provide high-performance techniques of peptides' databases partitioning where each parallel unit could search and rank locally and independently.