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chainCleaner improves genome alignment specificity and sensitivity.

Hernando G Suarez^1,2, Bjoern E Langer^1,2, Pradnya Ladde^1,2

¹Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.

Bioinformatics (Oxford, England)

|January 22, 2017

Summary

This summary is machine-generated.

chainCleaner enhances genome alignments by removing spurious local alignments that obscure evolutionary history. This method improves gene alignment and recovers significant genomic data, advancing comparative genomics.

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Area of Science:

Genomics
Bioinformatics
Evolutionary Biology

Background:

Accurate genome alignments are essential for comparative genomics.
Genomic rearrangements pose challenges to sensitive and accurate genome alignment.

Purpose of the Study:

To present chainCleaner, a fast computational approach to improve genome alignment specificity.
To accurately detect and remove local alignments that obscure evolutionary history.

Main Methods:

The chainCleaner algorithm was developed to refine genome alignments.
Systematic tests were performed on alignments between human and other vertebrate genomes.

Main Results:

chainCleaner improves the alignment of orthologous genes.
It unmasks gene exon alignments previously obscured by pseudogene alignments.
The method recovers substantial local alignments below standard score thresholds.

Conclusions:

chainCleaner enhances both the sensitivity and specificity of genome alignments.
This approach has broad applicability in comparative genomics research.
The tool is available for use and further development.