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Sharma, V. ; Hiller, M.*

Coding exon-structure aware realigner (CESAR): Utilizing genome Aaignments for comparative gene annotation.

In: Gene Prediction. Berlin [u.a.]: Springer, 2019. 179-191 (Methods Mol. Biol. ; 1962)
DOI PMC
Open Access Green as soon as Postprint is submitted to ZB.
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 .
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Publication type Article: Edited volume or book chapter
Keywords Cesar ; Comparative Gene Annotation ; Genome Alignment ; Splice Site Shift
ISSN (print) / ISBN 1064-3745
e-ISSN 1940-6029
Book Volume Title Gene Prediction
Journal Methods in Molecular Biology
Quellenangaben Volume: 1962, Issue: , Pages: 179-191 Article Number: , Supplement: ,
Publisher Springer
Publishing Place Berlin [u.a.]
Reviewing status Peer reviewed
Institute(s) Institute of Pancreatic Islet Research (IPI)