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Cited by 1Genome Rearrangement AlgorithmsGenomics and Phylogenetic StudiesChromosomal and Genetic Variations

Supporting data for "halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments"

Open access
Krasheninnikova, Ksenia, Diekhans, Mark, Armstrong, Joel, Dievskii, Aleksei, Paten, Benedict, O’Brien, Stephen, J·2020·GigaScience Database
DOI 10.5524/100740
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Abstract

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 based on whole-genome, reference-free alignments. Very large multiple alignments of full-genome sequences stored in a binary format demand an accurate and efficient computational approach for synteny blocks 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/.

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DataCite · 10.5524/100740

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  • Comparison of gene-level orthology between cat chromosomes A1, B1, C1 and dog chromosomes 28 and 25 using OMA Browser supports the conclusions of inference derived by halSynteny.

    “Comparison of gene-level orthology performed between the cat chromosomes A1, B1, and C1 and dog chromosomes 28 and 25 [23] using OMA Browser [24,25] support the conclusions of inference derived by halSynteny.”

    From halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments (2020) · cites this paper as [23]

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Authors
Krasheninnikova, K., Diekhans, M., Armstrong, J., Dievskii, A., Paten, B., & O’Brien, S.
ORCID
Venue
GigaScience Database
Publisher
GigaScience Database
Published
2020
DOI
10.5524/100740
OpenAlex
W6913121808
Cited by
0
References
0
Type
dataset
Language
en
Open access
Licence
Locations
GigaDB (public-domain)
Funders
  • National Institute of Health (2U41HG007234-05)
  • National Human Genome Research Institute (R01HG008742)
  • Russian Science Foundation (17-14-01138)
  • Saint Petersburg State University (1.52.1647.2016)
  • Russian Foundation for Basic Research (20-34-70055)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
chromosomal rearrangements, comparative genomics, vertebrate genomes

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