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Noncoding RNA transcription beyond annotated genes
Current Opinion in Genetics & Development, 2007Recent analyses based on high-throughput transcriptome data have revealed that the fraction of the genome that is transcribed largely exceeds the fraction encoding protein. Transcription of unconventional genes into noncoding RNAs is widespread and, in mammals, these RNAs comprise at least half the total number of RNAs transcribed by RNA polymerase II.
Piero, Carninci, Yoshihide, Hayashizaki
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Protozoan genomes: gene identification and annotation
International Journal for Parasitology, 2005The draft sequence of several complete protozoan genomes is now available and genome projects are ongoing for a number of other species. Different strategies are being implemented to identify and annotate protein coding and RNA genes in these genomes, as well as study their genomic architecture.
E A, Worthey, P J, Myler
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COGNATE: Comparative Gene Annotation Characterizer
2019Comprehensive structural characterization of protein-coding gene repertoires is a crucial step to identify differences and commonalities in comparative genomics contexts. This requires a descriptive set of standardized parameters as well as summary statistics of, e.g., gene lengths and exon counts. We developed the tool COGNATE to gather this data from
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Visual annotation of the gene database
2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2009The genes in NCBI databases are currently annotated with itemized text (Gene Reference Into Function, or GeneRIF). A previous work suggests that the visual presentation can be more effective when time and space are under heavy constraints. Here we report a novel annotation of the genome information using Web 2.0 technologies: GeneGIF (Gene Graphics ...
Jing, Wen +4 more
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Mass spectrometry‐based prokaryote gene annotation
PROTEOMICS, 2007AbstractMS combined with database searching has become the preferred method for identifying proteins present in cell or tissue samples. The technique enables us to execute large‐scale proteome analyses of species whose genomes have already been sequenced.
Yoko, Ishino +3 more
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A Dictionary-Based Approach for Gene Annotation
Journal of Computational Biology, 1999This paper describes a fast and fully automated dictionary-based approach to gene annotation and exon prediction. Two dictionaries are constructed, one from the nonredundant protein OWL database and the other from the dbEST database. These dictionaries are used to obtain O (1) time lookups of tuples in the dictionaries (4 tuples for the OWL database ...
Pachter, Lior +6 more
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Manual Gene Curation and Functional Annotation
2018No genome sequencing project is complete without structural and functional annotation. Gene models and functional predictions for these models can be obtained relatively easily using computational methods, but they are prone to errors. We describe herein the steps we use to manually curate gene models and functionally annotate them.
McDonnell, Erin +2 more
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Cancer epigenetics in clinical practice
Ca-A Cancer Journal for Clinicians, 2023Veronica Davalos, Manel Esteller
exaly