Evidence
Bioinformatics. 2024 Aug 17:btae517. doi: 10.1093/bioinformatics/btae517. Online ahead of print.
ABSTRACT
MOTIVATION: Spaln is the earliest practical tool for self-sufficient genome mapping and spliced alignment of protein query sequences onto a mammalian-sized eukaryotic genomic sequence. However, its computational speed has become inadequate for the analysis of rapidly growing genomic and transcript sequence data.
RESULTS: The dynamic programming calculation of Spaln has been sped up in two ways: 1) the introduction of the multi-intermediate unidirectional Hirschberg method and 2) SIMD-based vectorization. The new version, Spaln3, is approximately seven times faster than the latest Spaln version 2, and its gene prediction accuracy is consistently higher than that of Miniprot.
AVAILABILITY AND IMPLEMENTATION: Https://github.com/ogotoh/spaln.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
PMID:39152995 | DOI:10.1093/bioinformatics/btae517
Estimated reading time: 3 minute(s)
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