Coding Exon-structure aware realigner (CESAR): Utilizing genome alignments for comparative gene annotation

Virag Sharma, Michael Hiller

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

Abstract

Alignment-based gene identification methods utilize sequence conservation between orthologous protein-coding genes to annotate genes in newly sequenced genomes. CESAR is an approach that makes use of existing genome alignments to transfer genes from one genome to other aligned genomes, and thus generates comparative gene annotations. To accurately detect conserved exons that exhibit an intact reading frame and consensus splice sites, CESAR produces a new alignment between orthologous exons, taking information about the exon’s reading frame and splice site positions into account. Furthermore, CESAR is able to detect most evolutionary splice site shifts, which helps to annotate exon boundaries at high precision. Here, we describe how to apply CESAR to generate comparative gene annotations for one or many species, and discuss the strengths and limitations of this approach. CESAR is available at https://github.com/hillerlab/CESAR2.0.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages179-191
Number of pages13
DOIs
Publication statusPublished - 2019
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume1962
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • CESAR
  • Comparative gene annotation
  • Genome alignment
  • Splice site shift

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