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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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2009
Gene annotation used to refer to the prediction and annotation of a coding transcript on a region of the genome, but as the complexity of the functional features on the genome increases, users require prediction of noncoding RNAs, alternatively spliced transcripts, pseudogenes, and conserved elements. Eight years after the initial draft sequence of the
Jennifer Harrow, Laurens G. Wilming
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Gene annotation used to refer to the prediction and annotation of a coding transcript on a region of the genome, but as the complexity of the functional features on the genome increases, users require prediction of noncoding RNAs, alternatively spliced transcripts, pseudogenes, and conserved elements. Eight years after the initial draft sequence of the
Jennifer Harrow, Laurens G. Wilming
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Bioinformatics: Databasing and Gene Annotation
2008"Omics" experiments amass large amounts of data requiring integration of several data sources for data interpretation. For instance, microarray, metabolomic, and proteomic experiments may at most yield a list of active genes, metabolites, or proteins, respectively. More generally, the experiments yield active features that represent subsequences of the
Lyle D. Burgoon, Timothy R. Zacharewski
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Gene Structure Annotation at PlantGDB
2007The accurate identification of exons and introns that comprise a complete plant gene structure can be a time-consuming and challenging task. Novel Web-based tools facilitate the process by providing a convenient interface to current transcript evidence, and portals to relevant bioinformatics software.
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Gene Identification and Structure Annotation
2021Rice (O. sativa L.) is one among the necessary food crops worldwide. Due to ever-increasing demand, many are undertaking several efforts to enhance its productivity - the latest being the sequel of Rice genome sequencing projects. The accelerated developments in next-generation sequencing (NGS) has bolstered these efforts in hundreds to thousands of ...
N. Sathyanarayana +2 more
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Gene Annotation and Pathway Mapping in KEGG
2007KEGG is a database resource (http://www.genome.jp/kegg/) that provides all knowledge about genomes and their relationships to biological systems such as cells and whole organisms as well as their interactions with the environment. KEGG is categorized in terms of building blocks in the genomic space, known as KEGG GENES, the chemical space, KEGG LIGAND,
Kiyoko F. Aoki-Kinoshita +1 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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Community-based gene structure annotation
Trends in Plant Science, 2005Uncertainty and inconsistency of gene structure annotation remain limitations on research in the genome era, frustrating both biologists and bioinformaticians, who have to sort out annotation errors for their genes of interest or to generate trustworthy datasets for algorithmic development. It is unrealistic to hope for better software solutions in the
Shannon D. Schlueter +4 more
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Applying the Gene Ontology in microbial annotation
Trends in Microbiology, 2009The ever-increasing number of microbial sequencing projects necessitates a standardized system for the capture of genomic data to ensure that the flood of information produced can be effectively utilized. The Gene Ontology (GO) provides the standard for gene product annotations in the areas of molecular function, biological process and cellular ...
Candace W Collmer +3 more
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Function Annotation in Gene Networks
2011Modern sequencing technology enables the discovery of new gene products in an increasing number of organisms. However, the sequence on its own does not provide sufficient information about cellular mechanisms and their function. Efforts need to be directed toward genome characterization at the molecular level.
Kathy Macropol +2 more
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