Using NCBI Resources for Gene Discovery

Slides: Web or PowerPoint versions

Kim D. Pruitt, Richa Agarwala, Hsiu-Chuan Chen, Slava Chetvernin, Deanna Church, Olga Ermolaeva, Wonhee Jang, Paul Kitts, Jonathan Kans, David Lipman, Jim Ostell, Sergey Resenchuk, Greg Schuler, Lynn Schriml, Steve Sherry, Tatiana Tatusova, Lukas Wagner, Sarah Wheelan, NCBI, Bethesda, MD

1. RefSeq Information:
   http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html
2. Human Genome Resources:
   http://www.ncbi.nlm.nih.gov/genome/guide/human/
3. Genome Assembly and Annotation Process:
   http://www.ncbi.nlm.nih.gov/genome/guide/build.html

NCBI provides several resources that support gene discovery including RefSeq sequence standards,  the LocusLink gene-centered description database, UniGene clustering of related transcripts,  HomoloGene computed homologous clusters, and comparative maps to the assembled and annotated human genome sequence displayed in the Map Viewer. The RefSeq project provides a non-redundant database of sequence standards through several methods including automated pipelines,  manual curation, collaboration, and ab initio gene prediction on genome assemblies. Predicted model RefSeqs represent a data set which includes putative novel genes.  Companion resources provide additional information about related sequences, expression, function, and other attributes. Similarly, UniGene and HomoloGene data, which provide information about related sequences, can be mined computationally or manually, using the query interface, to identify novel genes.  The Map Viewer resource displays multiple sequence-based types of information including known genes, predicted genes, transcribed regions, markers, and variation features; these displays integrate several sources of information and provide a very powerful approach to identify genomic sequence data with novel coding potential. When used together, these resources provide a wealth of information about known and predicted genes and greatly facilitate identification of putative novel genes for further investigation.

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