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PxBLAT: An Ergonomic and Efficient Python Binding Library for BLAT

We introduce PxBLAT, a Python library designed to enhance usability and efficiency in interacting with the BLAST-like alignment tool (BLAT). PxBLAT provides an intuitive application programming interface (API) design, allowing the incorporation of its functionality directly into Python-based bioinfo...

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Detalles Bibliográficos
Autores principales: Li, Yangyang, Yang, Rendong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10418261/
https://www.ncbi.nlm.nih.gov/pubmed/37577677
http://dx.doi.org/10.1101/2023.08.02.551686
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author Li, Yangyang
Yang, Rendong
author_facet Li, Yangyang
Yang, Rendong
author_sort Li, Yangyang
collection PubMed
description We introduce PxBLAT, a Python library designed to enhance usability and efficiency in interacting with the BLAST-like alignment tool (BLAT). PxBLAT provides an intuitive application programming interface (API) design, allowing the incorporation of its functionality directly into Python-based bioinformatics workflows. Besides, it integrates seamlessly with Biopython and comes equipped with user-centric features like server readiness checks and port retry mechanisms. PxBLAT removes the necessity for system calls and intermediate files, as well as reducing latency and data conversion overhead. Benchmark tests reveal PxBLAT gains a ~20% performance boost compared to BLAT in the Python environment. Availability and Implementation: PxBLAT supports Python (version 3.9+), and pre-compiled packages are released via PyPI (https://pypi.org/project/pxblat/) and Bioconda (https://anaconda.org/bioconda/pxblat). The source code and executables are freely available for academic, nonprofit and personal use. Commercial licensing information is available on the Kent Informatics website (http://www.kentinformatics.com). Its documentation is available on ReadTheDocs (https://pxblat.readthedocs.io/en/latest/).
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spelling pubmed-104182612023-08-12 PxBLAT: An Ergonomic and Efficient Python Binding Library for BLAT Li, Yangyang Yang, Rendong bioRxiv Article We introduce PxBLAT, a Python library designed to enhance usability and efficiency in interacting with the BLAST-like alignment tool (BLAT). PxBLAT provides an intuitive application programming interface (API) design, allowing the incorporation of its functionality directly into Python-based bioinformatics workflows. Besides, it integrates seamlessly with Biopython and comes equipped with user-centric features like server readiness checks and port retry mechanisms. PxBLAT removes the necessity for system calls and intermediate files, as well as reducing latency and data conversion overhead. Benchmark tests reveal PxBLAT gains a ~20% performance boost compared to BLAT in the Python environment. Availability and Implementation: PxBLAT supports Python (version 3.9+), and pre-compiled packages are released via PyPI (https://pypi.org/project/pxblat/) and Bioconda (https://anaconda.org/bioconda/pxblat). The source code and executables are freely available for academic, nonprofit and personal use. Commercial licensing information is available on the Kent Informatics website (http://www.kentinformatics.com). Its documentation is available on ReadTheDocs (https://pxblat.readthedocs.io/en/latest/). Cold Spring Harbor Laboratory 2023-10-24 /pmc/articles/PMC10418261/ /pubmed/37577677 http://dx.doi.org/10.1101/2023.08.02.551686 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
Li, Yangyang
Yang, Rendong
PxBLAT: An Ergonomic and Efficient Python Binding Library for BLAT
title PxBLAT: An Ergonomic and Efficient Python Binding Library for BLAT
title_full PxBLAT: An Ergonomic and Efficient Python Binding Library for BLAT
title_fullStr PxBLAT: An Ergonomic and Efficient Python Binding Library for BLAT
title_full_unstemmed PxBLAT: An Ergonomic and Efficient Python Binding Library for BLAT
title_short PxBLAT: An Ergonomic and Efficient Python Binding Library for BLAT
title_sort pxblat: an ergonomic and efficient python binding library for blat
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10418261/
https://www.ncbi.nlm.nih.gov/pubmed/37577677
http://dx.doi.org/10.1101/2023.08.02.551686
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