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bioRxiv · 10.1101/2023.08.02.551686

PxBLAT: An Ergonomic and Efficient Python Binding Library for BLAT

Li, Y.·Yang, R.
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Abstract

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. Moreover, PxBLATs design philosophy emphasizes ease of use, memory efficiency, and the elimination of intermediary files and unnecessary system calls, thereby enhancing computational speed and user experience. Benchmark tests reveal its superior performance across various datasets, illustrating its capacity to maintain correctness. 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 executable are freely available for academic, nonprofit, and personal use. Its documentation is available on ReadTheDocs (https://pxblat.readthedocs.io/en/latest/).

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Li, Y., Yang, R.. 2023-08-05. PxBLAT: An Ergonomic and Efficient Python Binding Library for BLAT. https://doi.org/10.1101/2023.08.02.551686

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