A1 Refereed original research article in a scientific journal

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




AuthorsSchmid Steven, Jeevannavar Aditya, Julian Timothy R., Tamminen Manu

PublisherPublic Library of Science

Publication year2023

JournalPLoS ONE

Journal name in sourcePLoS ONE

Article numbere0289693

Volume18

Issue11

ISSN1932-6203

eISSN1932-6203

DOIhttps://doi.org/10.1371/journal.pone.0289693

Web address https://doi.org/10.1371/journal.pone.0289693

Self-archived copy’s web addresshttps://research.utu.fi/converis/portal/detail/Publication/182416497


Abstract

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).


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Last updated on 2025-27-03 at 22:04