ExceS-A: an Exon-centric Split Aligner

Overview

Journal J Integr Bioinform

Specialty Biology

Date 2022 Mar 7

PMID 35254744

Authors

Franziska Reinhardt

Peter F Stadler

Affiliations

Soon will be listed here.

Abstract

Spliced alignments are a key step in the construction of high-quality homology-based annotations of protein sequences. The exon/intron structure, which is computed as part of spliced alignment procedures, often conveys important information for the distinguishing paralogous members of gene families. Here we present an exon-centric pipeline for spliced alignment that is intended in particular for applications that involve exon-by-exon comparisons of coding sequences. We show that the simple, blat-based approach has advantages over established tools in particular for genes with very large introns and applications to fragmented genome assemblies.

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