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. 2000 Jan 1;28(1):141-5.
doi: 10.1093/nar/28.1.141.

The TIGR gene indices: reconstruction and representation of expressed gene sequences

J Quackenbush  1 , F Liang, I Holt, G Pertea, J Upton
Affiliations

The TIGR gene indices: reconstruction and representation of expressed gene sequences

J Quackenbush et al. Nucleic Acids Res. .

Abstract

Expressed sequence tags (ESTs) have provided a first glimpse of the collection of transcribed sequences in a variety of organisms. However, a careful analysis of this sequence data can provide significant additional functional, structural and evolutionary information. Our analysis of the public EST sequences, available through the TIGR Gene Indices (TGI; http://www.tigr.org/tdb/tdb.html ), is an attempt to identify the genes represented by that data and to provide additional information regarding those genes. Gene Indices are constructed for selected organisms by first clustering, then assembling EST and annotated gene sequences from GenBank. This process produces a set of unique, high-fidelity virtual transcripts, or tentative consensus (TC) sequences. The TC sequences can be used to provide putative genes with functional annotation, to link the transcripts to mapping and genomic sequence data, and to provide links between orthologous and paralogous genes.

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Figures

Figure 1
Figure 1
An example THC from the Human Gene Index. The consensus sequence is presented in FASTA format below which the locations of the gene sequence (HT27821; insulin receptor inhibitor, muscle) and ESTs that comprise the assembly are shown with their respective locations within the assembly. Links are provided to GenBank records, internal data for all ESTs sequenced at TIGR and to clones available through the ATCC. This THC has been assigned a putative ID of ‘insulin receptor inhibitor, muscle’ as it contains HT27821, an expressed sequence constructed from GenBank CDS features and contained within the EGAD database. This THC also includes Radiation Hybrid mapping data derived from Gene Map ’98 (14).
See this image and copyright information in PMC

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