Portable BLAST-like algorithm library and its implementations for command line, Python, and R

• Published in: PloS one Vol. 18; no. 11; p. e0289693
• Main Authors: Schmid, Steven, Jeevannavar, Aditya, Julian, Timothy R, Tamminen, Manu
• Format: Journal Article
• Language: English
• Published: San Francisco, CA USA Public Library of Science 30.11.2023; Public Library of Science (PLoS)
• Subjects: Algorithms; Amino acid sequence; Amino acids; Analysis; Biology and Life Sciences; Computational biology; Computer and Information Sciences; DNA sequencing; Engineering and Technology; Explosions; Methods; Nucleotide sequencing; Phylogeny; Python (Programming language); R (Programming language); Research and analysis methods; RNA sequencing; Technology application; Switzerland
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0289693

Basic local-alignment search tool (BLAST) is a versatile and commonly used sequence analysis tool in bioinformatics. BLAST permits fast and flexible sequence similarity searches across nucleotide and amino acid sequences, leading to diverse applications such as protein domain identification, orthology searches, and phylogenetic annotation. Most BLAST implementations are command line tools which produce output as comma-separated values files. However, a portable, modular and embeddable implementation of a BLAST-like algorithm, is still missing from our toolbox. Here we present nsearch, a command line tool and C++11 library which provides BLAST-like functionality that can easily be embedded in any application. As an example of this portability we present Blaster which leverages nsearch to provide native BLAST-like functionality for the R programming language, as well as npysearch which provides similar functionality for Python. These packages permit embedding BLAST-like functionality into larger frameworks such as Shiny or Django applications. Benchmarks show that nsearch, npysearch, and Blaster are comparable in speed and accuracy to other commonly used modern BLAST implementations such as VSEARCH and BLAST+. We envision similar implementations of nsearch for other languages commonly used in data science such as Julia to facilitate sequence similarity comparisons. Nsearch, Blaster and npysearch are free to use under the BSD 3.0 license and available on Github Conda, CRAN (Blaster) and PyPi (npysearch).