Spaln3: improvement in speed and accuracy of genome mapping and spliced alignment of protein query sequences.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 39152995.
- Also identified by DOI 10.1093/bioinformatics/btae517 and PMC identifier 11361809.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. The dynamic programming calculation of Spaln has been sped up in two ways: (i) the introduction of the multi-intermediate unidirectional Hirschberg method and (ii) SIMD-based vectorization. The new version, Spaln3, is ∼7 times faster than the latest Spaln version 2, and its gene prediction accuracy is consistently higher than that of Miniprot. https://github.com/ogotoh/spaln.
Medical subject headings
- Software
- Chromosome Mapping