Poster: Bioinformatics
Abs #
861: Plant gene indices: integrating ESTs, genes, and genomes
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Presenter: |
Lee, Dan , dlee@tigr.org |
Authors | Lee, Dan (A) Tsai, Jennifer (A) Sunkara, Sirisha (A) Cheung, Foo (A) Chan, Agnes (A) Sultana, Razvan (A) Pertea, Geo (A) Antonescu, Valentin (A) Karamycheva, Svetlana (A) Quackenbush, John (A) | | Affiliations: |
(A): The Institute for Genomic Research
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While genome sequencing projects are advancing rapidly, EST sequencing and analysis remains a primary research tool for the identification and categorization of transcribed genes in a wide variety of species and an important resource for the annotation of genomic sequences. The ESTs, known genes, predicted gene transcripts, and available mapping and sequencing data have been integrated together to build a cross-genome reference database. TIGR Gene Indices (TGI; ) are a collection of species-specific databases that use a highly refined protocol to analyze EST sequences in an attempt to identify the genes represented within the EST data and to provide structural and functional information regarding those genes. Gene Indices are constructed by first comparing, clustering, then assembling EST and gene sequences (ET) from GenBank for the targeted species. This process produces a set of unique, high-fidelity virtual transcripts, or Tentative Consensus (TC) sequences. There are 22 plant gene indices with over 300,000 TCs available now for major economically and biologically important plants including Arabidopsis, pine, cotton, lotus, lettuce, sunflower, tomato, potato, Nicotiana benthami, soybean, Medicago, ice plant, grape, onion, rice, maize, wheat, Sorghum bicolor, barley, rye, sugarcane, and green alga Chlamydomonas reinhardtii. The TC sequences can be used to provide putative genes with functional annotation, to link the transcripts to genetic and physical maps, and genomic sequence data, to enhance phylogenic analyses between orthologous genes, to provide the unique oligo dataset for functional genomics, to study the sequence variations and polymorphisms, and as a resource for comparative sequence analysis.
