Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation.
Virag Sharma1,2, Michael Hiller1,2
1Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
Nucleic Acids Research
|June 25, 2017
Summary
Increasing genome alignment sensitivity reveals thousands of novel gene annotations, especially for distantly related species. This enhanced comparative genomics approach improves gene and exon detection in vertebrates.
Area of Science:
- Comparative genomics
- Bioinformatics
- Evolutionary biology
Background:
- Genome alignments are crucial for transferring gene annotations between species.
- Annotation completeness relies heavily on the sensitivity of genome alignment methods.
Purpose of the Study:
- To investigate the impact of genome alignment parameters on comparative gene annotation.
- To determine if increased alignment sensitivity improves the detection of novel orthologous exons and genes.
Main Methods:
- Systematic testing of genome alignment parameters for sensitivity.
- Construction of a multiple genome alignment of 144 vertebrate species.
- Utilizing the CESAR tool to map human genes to other vertebrates based on the alignment.
Main Results:
- Higher alignment sensitivity identified thousands of previously missed orthologous exon alignments.
- Comparative gene annotation completeness significantly improved, adding an average of 2382 novel exons and 117 novel genes in mammals.
- Non-mammalian species saw even greater improvements, with an average of 7440 novel exons and 317 novel genes.
Conclusions:
- A more sensitive genome alignment strategy is recommended for comparisons between distantly related species.
- The study provides a valuable resource of a 144-vertebrate genome alignment and comparative gene annotations.
- Enhanced alignment sensitivity substantially boosts the discovery of novel genes and exons in comparative genomics studies.
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