PxBLAT: an efficient python binding library for BLAT
Abstract Background With the surge in genomic data driven by advancements in sequencing technologies, the demand for efficient bioinformatics tools for sequence analysis has become paramount. BLAST-like alignment tool (BLAT), a sequence alignment tool, faces limitations in performance efficiency and...
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BMC
2024-06-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-024-05844-0 |
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| author | Yangyang Li Rendong Yang |
| author_facet | Yangyang Li Rendong Yang |
| author_sort | Yangyang Li |
| collection | DOAJ |
| description | Abstract Background With the surge in genomic data driven by advancements in sequencing technologies, the demand for efficient bioinformatics tools for sequence analysis has become paramount. BLAST-like alignment tool (BLAT), a sequence alignment tool, faces limitations in performance efficiency and integration with modern programming environments, particularly Python. This study introduces PxBLAT, a Python-based framework designed to enhance the capabilities of BLAT, focusing on usability, computational efficiency, and seamless integration within the Python ecosystem. Results PxBLAT demonstrates significant improvements over BLAT in execution speed and data handling, as evidenced by comprehensive benchmarks conducted across various sample groups ranging from 50 to 600 samples. These experiments highlight a notable speedup, reducing execution time compared to BLAT. The framework also introduces user-friendly features such as improved server management, data conversion utilities, and shell completion, enhancing the overall user experience. Additionally, the provision of extensive documentation and comprehensive testing supports community engagement and facilitates the adoption of PxBLAT. Conclusions PxBLAT stands out as a robust alternative to BLAT, offering performance and user interaction enhancements. Its development underscores the potential for modern programming languages to improve bioinformatics tools, aligning with the needs of contemporary genomic research. By providing a more efficient, user-friendly tool, PxBLAT has the potential to impact genomic data analysis workflows, supporting faster and more accurate sequence analysis in a Python environment. |
| format | Article |
| id | doaj-art-0c1ef74c41884e20b5c879caa01562b0 |
| institution | DOAJ |
| issn | 1471-2105 |
| language | English |
| publishDate | 2024-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-0c1ef74c41884e20b5c879caa01562b02025-08-20T02:50:04ZengBMCBMC Bioinformatics1471-21052024-06-012511810.1186/s12859-024-05844-0PxBLAT: an efficient python binding library for BLATYangyang Li0Rendong Yang1Department of Urology, Northwestern University Feinberg School of MedicineDepartment of Urology, Northwestern University Feinberg School of MedicineAbstract Background With the surge in genomic data driven by advancements in sequencing technologies, the demand for efficient bioinformatics tools for sequence analysis has become paramount. BLAST-like alignment tool (BLAT), a sequence alignment tool, faces limitations in performance efficiency and integration with modern programming environments, particularly Python. This study introduces PxBLAT, a Python-based framework designed to enhance the capabilities of BLAT, focusing on usability, computational efficiency, and seamless integration within the Python ecosystem. Results PxBLAT demonstrates significant improvements over BLAT in execution speed and data handling, as evidenced by comprehensive benchmarks conducted across various sample groups ranging from 50 to 600 samples. These experiments highlight a notable speedup, reducing execution time compared to BLAT. The framework also introduces user-friendly features such as improved server management, data conversion utilities, and shell completion, enhancing the overall user experience. Additionally, the provision of extensive documentation and comprehensive testing supports community engagement and facilitates the adoption of PxBLAT. Conclusions PxBLAT stands out as a robust alternative to BLAT, offering performance and user interaction enhancements. Its development underscores the potential for modern programming languages to improve bioinformatics tools, aligning with the needs of contemporary genomic research. By providing a more efficient, user-friendly tool, PxBLAT has the potential to impact genomic data analysis workflows, supporting faster and more accurate sequence analysis in a Python environment.https://doi.org/10.1186/s12859-024-05844-0Software librariesSequence analysisBLAT |
| spellingShingle | Yangyang Li Rendong Yang PxBLAT: an efficient python binding library for BLAT BMC Bioinformatics Software libraries Sequence analysis BLAT |
| title | PxBLAT: an efficient python binding library for BLAT |
| title_full | PxBLAT: an efficient python binding library for BLAT |
| title_fullStr | PxBLAT: an efficient python binding library for BLAT |
| title_full_unstemmed | PxBLAT: an efficient python binding library for BLAT |
| title_short | PxBLAT: an efficient python binding library for BLAT |
| title_sort | pxblat an efficient python binding library for blat |
| topic | Software libraries Sequence analysis BLAT |
| url | https://doi.org/10.1186/s12859-024-05844-0 |
| work_keys_str_mv | AT yangyangli pxblatanefficientpythonbindinglibraryforblat AT rendongyang pxblatanefficientpythonbindinglibraryforblat |