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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 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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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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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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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.
Elizabeth A. Worthey, Peter J. Myler
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Gene Family Prediction and Annotation
2016A well-annotated genome is necessary for the rapid identification of genes in the genome, gene mapping and functional analysis. The arrangement of any genome has typically taken many years, but with new sequencing methodologies, the time to produce genomes is greatly reduced; however, with this increased speed, there has been a deterioration in the ...
Sarah M. Pilkington, Robert J. Schaffer
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Mycoplasma genes: a case for reflective annotation
Trends in Microbiology, 1997Although function can be assigned to genome sequence by homology at a macroscopic level, this can be misleading in the absence of data on enzyme activities. Together, such data can reveal whether open reading frames are expressed, identify multienzyme function and point to 'orphan' function.
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