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

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, ref...

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Autores principales: Krasheninnikova, Ksenia, Diekhans, Mark, Armstrong, Joel, Dievskii, Aleksei, Paten, Benedict, O’Brien, Stephen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7254927/
https://www.ncbi.nlm.nih.gov/pubmed/32463100
http://dx.doi.org/10.1093/gigascience/giaa047
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author Krasheninnikova, Ksenia
Diekhans, Mark
Armstrong, Joel
Dievskii, Aleksei
Paten, Benedict
O’Brien, Stephen
author_facet Krasheninnikova, Ksenia
Diekhans, Mark
Armstrong, Joel
Dievskii, Aleksei
Paten, Benedict
O’Brien, Stephen
author_sort Krasheninnikova, Ksenia
collection PubMed
description 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/.
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spelling pubmed-72549272020-06-03 halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments Krasheninnikova, Ksenia Diekhans, Mark Armstrong, Joel Dievskii, Aleksei Paten, Benedict O’Brien, Stephen Gigascience Technical Note 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/. Oxford University Press 2020-05-28 /pmc/articles/PMC7254927/ /pubmed/32463100 http://dx.doi.org/10.1093/gigascience/giaa047 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Technical Note
Krasheninnikova, Ksenia
Diekhans, Mark
Armstrong, Joel
Dievskii, Aleksei
Paten, Benedict
O’Brien, Stephen
halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments
title halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments
title_full halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments
title_fullStr halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments
title_full_unstemmed halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments
title_short halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments
title_sort halsynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments
topic Technical Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7254927/
https://www.ncbi.nlm.nih.gov/pubmed/32463100
http://dx.doi.org/10.1093/gigascience/giaa047
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