We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
Spaln3: improvement in speed and accuracy of genome mapping and spliced alignment of protein query sequences.
- Authors
Gotoh, Osamu
- 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: (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. Availability and implementation https://github.com/ogotoh/spaln.
- Subjects
GENE mapping; AMINO acid sequence; DYNAMIC programming; SPEED; MOTIVATION (Psychology)
- Publication
Bioinformatics, 2024, Vol 40, Issue 8, p1
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btae517