A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä
Portable BLAST-like algorithm library and its implementations for command line, Python, and R
Tekijät: Schmid Steven, Jeevannavar Aditya, Julian Timothy R., Tamminen Manu
Kustantaja: Public Library of Science
Julkaisuvuosi: 2023
Journal: PLoS ONE
Tietokannassa oleva lehden nimi: PLoS ONE
Artikkelin numero: e0289693
Vuosikerta: 18
Numero: 11
ISSN: 1932-6203
eISSN: 1932-6203
DOI: https://doi.org/10.1371/journal.pone.0289693
Verkko-osoite: https://doi.org/10.1371/journal.pone.0289693
Rinnakkaistallenteen osoite: https://research.utu.fi/converis/portal/detail/Publication/182416497
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).
Ladattava julkaisu This is an electronic reprint of the original article. |