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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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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/. |
format | Online Article Text |
id | pubmed-7254927 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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