ArticleNucleic acids research2016
Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 58 citations in OpenAlex.
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- Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas.Current biology : CB · 2022Article
- Cross-species examination of X-chromosome inactivation highlights domains of escape from silencing.Epigenetics & chromatin · 2021Article
- PseudoChecker: an integrated online platform for gene inactivation inference.Nucleic acids research · 2020Article
- Losses of human disease-associated genes in placental mammals.NAR genomics and bioinformatics · 2020Article
- A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae).GigaScience · 2020Article
- A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers.GigaScience · 2020Article
- Evolutionary Analysis of Bile Acid-Conjugating Enzymes Reveals a Complex Duplication and Reciprocal Loss History.Genome biology and evolution · 2019Article
- Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations.Science advances · 2019Article
- Signatures of Relaxed Selection in the CYP8B1 Gene of Birds and Mammals.Journal of molecular evolution · 2019Article
- Complete Inactivation of Sebum-Producing Genes Parallels the Loss of Sebaceous Glands in Cetacea.Molecular biology and evolution · 2019Article
- Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes.
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