2023 journal article

POInTbrowse: orthology prediction and synteny exploration for paleopolyploid genomes

BMC BIOINFORMATICS, 24(1).

By: M. Siddiqui n & G. Conant n 

author keywords: POInT; Comparative genomics; Browser
MeSH headings : Humans; Synteny; Phylogeny; Genome; Genomics; Polyploidy; Evolution, Molecular
TL;DR: POInT_browse is described, a web portal that gives access to the orthology inferences made for polyploid genomes with POInT, the Polyploidy Orthology Inference Tool, allowing users to visualize genomic regions produced bypolyploidies and perform batch queries for each polyPLoidy event. (via Semantic Scholar)
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AbstractWe describe POInTbrowse, a web portal that gives access to the orthology inferences made for polyploid genomes with POInT, the Polyploidy Orthology Inference Tool. Ancient, or paleo-, polyploidy events are widely distributed across the eukaryotic phylogeny, and the combination of duplicated and lost duplicated genes that these polyploidies produce can confound the identification of orthologous genes between genomes. POInT uses conserved synteny and phylogenetic models to infer orthologous genes between genomes with a shared polyploidy. It also gives confidence estimates for those orthology inferences. POInTbrowsegives both graphical and query-based access to these inferences from 12 different polyploidy events, allowing users to visualize genomic regions produced by polyploidies and perform batch queries for each polyploidy event, downloading genes trees and coding sequences for orthologous genes meeting user-specified criteria. POInTbrowseand the associated data are online athttps://wgd.statgen.ncsu.edu.