Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon.

ABSTRACT: A significant portion of genes in vertebrate genomes belongs to multigene families, with each family containing several gene copies whose presence/absence, as well as isoform structure, can be highly variable across individuals. Existing de novo techniques for assaying the sequences of such highly-similar gene families fall short of reconstructing end-to-end transcripts with nucleotide-level precision or assigning alternatively spliced transcripts to their respective gene copies. We present IsoCon, a high-precision method using long PacBio Iso-Seq reads to tackle this challenge. We apply IsoCon to nine Y chromosome ampliconic gene families and show that it outperforms existing methods on both experimental and simulated data. IsoCon has allowed us to detect an unprecedented number of novel

SUBMITTER: Sahlin K 

PROVIDER: S-EPMC6214943 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature