halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments.
HAL format
Synteny blocks
comparative genomics
genome alignments
Journal
GigaScience
ISSN: 2047-217X
Titre abrégé: Gigascience
Pays: United States
ID NLM: 101596872
Informations de publication
Date de publication:
01 06 2020
01 06 2020
Historique:
received:
07
12
2019
revised:
16
03
2020
accepted:
18
04
2020
entrez:
29
5
2020
pubmed:
29
5
2020
medline:
5
10
2021
Statut:
ppublish
Résumé
Large-scale sequencing projects provide high-quality full-genome data that can be used for reconstruction of chromosomal exchanges and rearrangements that disrupt conserved syntenic blocks. The highest resolution of cross-species homology can be obtained on the basis of whole-genome, reference-free alignments. Very large multiple alignments of full-genome sequence stored in a binary format demand an accurate and efficient computational approach for synteny block production. halSynteny performs efficient processing of pairwise alignment blocks for any pair of genomes in the alignment. The tool is part of the HAL comparative genomics suite and is targeted to build synteny blocks for multi-hundred-way, reference-free vertebrate alignments built with the Cactus system. halSynteny enables an accurate and rapid identification of synteny in multiple full-genome alignments. The method is implemented in C++11 as a component of the halTools software and released under MIT license. The package is available at https://github.com/ComparativeGenomicsToolkit/hal/.
Sections du résumé
BACKGROUND
Large-scale sequencing projects provide high-quality full-genome data that can be used for reconstruction of chromosomal exchanges and rearrangements that disrupt conserved syntenic blocks. The highest resolution of cross-species homology can be obtained on the basis of whole-genome, reference-free alignments. Very large multiple alignments of full-genome sequence stored in a binary format demand an accurate and efficient computational approach for synteny block production.
FINDINGS
halSynteny performs efficient processing of pairwise alignment blocks for any pair of genomes in the alignment. The tool is part of the HAL comparative genomics suite and is targeted to build synteny blocks for multi-hundred-way, reference-free vertebrate alignments built with the Cactus system.
CONCLUSIONS
halSynteny enables an accurate and rapid identification of synteny in multiple full-genome alignments. The method is implemented in C++11 as a component of the halTools software and released under MIT license. The package is available at https://github.com/ComparativeGenomicsToolkit/hal/.
Identifiants
pubmed: 32463100
pii: 5848161
doi: 10.1093/gigascience/giaa047
pmc: PMC7254927
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NHGRI NIH HHS
ID : U41 HG007234
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG008742
Pays : United States
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press.
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