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AlignBucket: a tool to speed up 'all-against-all' protein sequence alignments optimizing length constraints

Giuseppe Profiti1, Piero Fariselli2, Rita Casadio3

  • 1Department of Computer Science and Engineering, via Mura Anteo Zamboni 7, Bologna, Bologna Biocomputing group, via S. Giacomo 9/2, Bologna and Health Sciences and Technologies ICIR, via Tolara di Sopra 41/E, Ozzano dell'Emilia, Italy.

Bioinformatics (Oxford, England)
|August 2, 2015
PubMed
Summary

This study introduces an optimized algorithm for partitioning large biological sequence databases. This method significantly speeds up sequence comparison, achieving a 5-fold improvement in real-world applications.

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