ArticleBMC bioinformatics2010
Parameters for accurate genome alignment.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 141 papers.
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141 citing papers in PubMed.
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- Telomere-to-telomere gap-free genome assembly provides genetic insight into the triterpenoid saponins biosynthesis inHorticulture research · 2025Article
- NEAR: Neural Embeddings for Amino acid Relationships.bioRxiv : the preprint server for biology · 2025Article
- Chromosome-scale genome assembly and annotation of Xenocypris argentea.Scientific data · 2025Article
- Chromosome-level genome assembly and annotation of the gynogenetic large-scale loach (Paramisgurnus dabryanus).Scientific data · 2025Article
- The telomere-to-telomere genome of flowering cherry (Prunus campanulata) reveals genomic evolution of the subgenus Cerasus.GigaScience · 2025Article
- Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species.Plant diversity · 2025Article
- Chromosome-level genome assembly of the medicinal insect Blaps rhynchopetera using Nanopore and Hi-C technologies.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- The macroevolutionary dynamics of pharyngognathy in fishes fail to support the key innovation hypothesis.Nature communications · 2024Article
81 more citing papers are in PubMed but not listed here.
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome sequence alignments form the basis of much research. Genome alignment depends on various mundane but critical choices, such as how to mask repeats and which score parameters to use. Surprisingly, there has been no large-scale assessment of these choices using real genomic data. Moreover, rigorous procedures to control the rate of spurious alignment have not been employed.
resultsWe have assessed 495 combinations of score parameters for alignment of animal, plant, and fungal genomes. As our gold-standard of accuracy, we used genome alignments implied by multiple alignments of proteins and of structural RNAs. We found the HOXD scoring schemes underlying alignments in the UCSC genome database to be far from optimal, and suggest better parameters. Higher values of the X-drop parameter are not always better. E-values accurately indicate the rate of spurious alignment, but only if tandem repeats are masked in a non-standard way. Finally, we show that gamma-centroid (probabilistic) alignment can find highly reliable subsets of aligned bases.
conclusionsThese results enable more accurate genome alignment, with reliability measures for local alignments and for individual aligned bases. This study was made possible by our new software, LAST, which can align vertebrate genomes in a few hours http://last.cbrc.jp/.
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