ArticleNucleic acids research2003
An organism-specific method to rank predicted coding regions in Trypanosoma brucei.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- "Eco-omics": a review of the application of genomics, transcriptomics, and proteomics for the study of the ecology of harmful algae.Microbial ecology · 2013Review
- Pathogenesis of chagas' disease: parasite persistence and autoimmunity.Clinical microbiology reviews · 2011Review
- Spliced leader RNA trans-splicing in dinoflagellates.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Systematic study of sequence motifs for RNA trans splicing in Trypanosoma brucei.Molecular and cellular biology · 2005Article
- A computational investigation of kinetoplastid trans-splicing.Genome biology · 2005Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Genome annotation in differently evolved organisms presents challenges because the lack of sequence-based homology limits the ability to determine the function of putative coding regions. To provide an alternative to annotation by sequence homology, we developed a method that takes advantage of unusual trypanosomatid biology and skews in nucleotide composition between coding regions and upstream regions to rank putative open reading frames based on the likelihood of coding. The method is 93% accurate when tested on known genes. We have applied our method to the full complement of open reading frames on Chromosome I of Trypanosoma brucei, and we can predict with high confidence that 226 putative coding regions are likely to be functional. Methods such as the one described here for discriminating true coding regions are critical for genome annotation when other sources of evidence for function are limited.
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