ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation. Issue 4 (17th December 2020)

• Record Type: Journal Article
• Authors: Arneson, Adriana; Felsheim, Brooke; Chien, Jennifer; Ernst, Jason
• Is Part Of: NAR genomics and bioinformatics. Volume 2:Issue 4(2020)
• Publication Date: 2020-12-17
• Subjects: Genomics -- Periodicals; Bioinformatics -- Periodicals; 572.8
• DOI: 10.1093/nargab/lqaa104
• Languages: English
• ISSNs: 2631-9268

Abstract

Abstract: ConsHMM is a method recently introduced to annotate genomes into conservation states, which are defined based on the combinatorial and spatial patterns of which species align to and match a reference genome in a multi-species DNA sequence alignment. Previously, ConsHMM was only applied to a single genome for one multi-species sequence alignment. Here, we apply ConsHMM to produce 22 additional genome annotations covering human and seven other organisms for a variety of multi-species alignments. Additionally, we extend ConsHMM to generate allele-specific annotations, which we use to produce conservation state annotations for every possible single-nucleotide mutation in the human genome. Finally, we provide a web interface to interactively visualize parameters and annotation enrichments for ConsHMM models. These annotations and visualizations comprise the ConsHMM Atlas, which we expect will be a valuable resource for analyzing a variety of major genomes and genetic variation.