chainCleaner improves genome alignment specificity and sensitivity

Suarez, Hernando; Langer , Bjoern E.; Ladde , Pradnya; Hiller, Michael

doi:10.1093/bioinformatics/btx024

Item

ITEM ACTIONSEXPORT

Add to Basket

Please note that a newer version of this item is available:
https://pure.mpg.de/pubman/item/item_2471686_4

DetailsSummary

Released

Journal Article

chainCleaner improves genome alignment specificity and sensitivity

MPS-Authors

/persons/resource/persons193004

Suarez, Hernando
Max Planck Institute for the Physics of Complex Systems, Max Planck Society;

/persons/resource/persons184581

Hiller, Michael
Max Planck Institute for the Physics of Complex Systems, Max Planck Society;

External Resource

https://academic.oup.com/bioinformatics/article/2929344
(Publisher version)

Fulltext (restricted access)

There are currently no full texts shared for your IP range.

Fulltext (public)

There are no public fulltexts stored in PuRe

Supplementary Material (public)

There is no public supplementary material available

Citation

Suarez, H., Langer, B. E., Ladde, P., & Hiller, M. (2017). chainCleaner improves genome alignment specificity and sensitivity. Bioinformatics, 33(11), 1596-1603. doi:10.1093/bioinformatics/btx024.

Cite as: https://hdl.handle.net/11858/00-001M-0000-002D-C6CA-C

Abstract

Motivation: Accurate alignments between entire genomes are crucial for comparative genomics. However, computing sensitive and accurate genome alignments is a challenging problem, complicated by genomic rearrangements. Results: Here we present a fast approach, called chainCleaner, that improves the specificity in genome alignments by accurately detecting and removing local alignments that obscure the evolutionary history of genomic rearrangements. Systematic tests on alignments between the human and other vertebrate genomes show that chainCleaner (i) improves the alignment of numerous orthologous genes, (ii) exposes alignments between exons of orthologous genes that were masked before by alignments to pseudogenes, and (iii) recovers hundreds of kilobases in local alignments that otherwise would fall below a minimum score threshold. Our approach has broad applicability to improve the sensitivity and specificity of genome alignments.