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Methods and strategies for gene structure curation in WormBase.

The Caenorhabditis elegans genome sequence was published over a decade ago; this was the first published genome of a multi-cellular organism and now the WormBase project has had a decade of experience in curating this genome's sequence and gene structures. In one of its roles as a central repository for nematode biology, WormBase continues to refine the gene structure annotations using sequence similarity and other computational methods, as well as information from the literature- and community-submitted annotations. We describe the various methods of gene structure curation that have been tried by WormBase and the problems associated with each of them. We also describe the current strategy for gene structure curation, and introduce the WormBase 'curation tool', which integrates different data sources in order to identify new and correct gene structures. Database URL: http://www.wormbase.org/.

Pubmed ID: 21543339 RIS Download

Mesh terms: Animals | Base Sequence | Caenorhabditis elegans | Computational Biology | DNA, Intergenic | Databases, Genetic | Genes, Helminth | High-Throughput Nucleotide Sequencing | Molecular Sequence Annotation | Open Reading Frames

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This is a list of tools and resources that we have found mentioned in this publication.


WormBase

A central data repository for nematode biology including the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes. Derived from the initial ACeDB database of C. elegans genetic and sequence information, WormBase includes the genomic, anatomical and functional information of C. elegans, other Caenorhabditis species and other nematodes. WormBase maintains a public FTP site where researchers can find many commonly requested files and datasets, the WormBase software and prepackaged databases.

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RepeatMasker

A software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ).

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