TY - JOUR

T1 - halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments

AU - Krasheninnikova, Ksenia

AU - Diekhans , Mark

AU - Armstrong, Joel

AU - Dievskii, Aleksei

AU - Paten, Benedict

AU - O'Brien, Stephen

PY - 2019

Y1 - 2019

N2 - 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/.

AB - 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/.

KW - HAL format

KW - Synteny blocks

KW - comparative genomics

KW - genome alignments

UR - https://pubmed.ncbi.nlm.nih.gov/32463100/

M3 - Article

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

ER -