ArticlebioRxiv : the preprint server for biology2024
PxBLAT: An efficient python binding library for BLAT.
Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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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, PxBLAT's 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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.