HALPER facilitates the identification of regulatory element orthologs across species

Abstract

Summary: Diverse traits have evolved through cis-regulatory changes in genome sequence that influence the magnitude, timing and cell type-specificity of gene expression. Advances in high-throughput sequencing and regulatory genomics have led to the identification of regulatory elements in individual species, but these genomic regions remain difficult to align across taxonomic orders due to their lack of sequence conservation relative to protein coding genes. The groundwork for tracing the evolution of regulatory elements is provided by the recent assembly of hundreds of genomes, the generation of reference-free Cactus multiple sequence alignments of these genomes, and the development of the halLiftover tool for mapping regions across these alignments. We present halLiftover Post-processing for the Evolution of Regulatory Elements (HALPER), a tool for constructing contiguous regulatory element orthologs from the outputs of halLiftover. We anticipate that this tool will enable users to efficiently identify orthologs of regulatory elements across hundreds of species, providing novel insights into the evolution of traits that have evolved through gene expression.

Availability and implementation: HALPER is implemented in python and available on github: https://github.com/pfenninglab/halLiftover-postprocessing.

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

HALPER overview. HALPER constructs contiguous orthologs from the outputs of halLiftover by first identifying the mapped fragment in the target species that contains the ortholog of the query species peak summit. It then extends the region until all mapped fragments on the same chromosome have been included. Putative target species orthologs are excluded if they do not meet user-specified criteria. Animal silhouettes were downloaded from http://phylopic.org/