The TIGR Gene Indices: reconstruction and representation of expressed gene sequences

By John Quackenbush, F. Liang, I. Holt, Geo Pertea, J. Upton. Nucleic Acids Res., 2000

362 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/d8e12220afcdb003d06893a0e8777d198c8c249e

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

In Plant Science

Citations in the corpus

The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species (2001, methodology): “However, the TIGR Gene Indices (4) are unique in the number of species surveyed, in the approach used to construct the individual species-specific databases and in the manner in which they can be used.”
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2007, methodology): “The largest section contains GOS- (A) The combined set of NCBI-nr, PG, TGI-EST, and ENS has 3,167,979 sequences.”
OrthoMCL: identification of ortholog groups for eukaryotic genomes. (2003, methodology): “An inflation index of I = 1.5 (where 86% of all groups are EC-consistent) appears to balance sensitivity and selectivity: exhibiting consistency close to the maximum observed value, while excluding a minimum number of sequences Clustering the entire data set at I = 1.5 yields 7265 groups from a…”
A hitchhiker's guide to expressed sequence tag (EST) analysis (2006, neutral): “referenced to mRNA or genomic sequences [72].”
GMD@CSB.DB: the Golm Metabolome Database (2005, background): “, 2003) and TIGR (Quackenbush et al., 2000), provide public access to protein sequences based on whole genome analyses, maps of protein–protein interactions, protein localization and many further features.”
RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome (2010, background): “Additionally, the genes identified in clade 2-1 with a Goslim molecular function of nutrient reservoir activity are part of the seed-filling process as most of these genes have functions based on the Dana Farber tentative consensus sequence [29,44] that include glycinin, beta-conglycinin and sucrose”
A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. (2003, methodology): “Because there is significant heterogeneity in the rate of amino acid substitutions among different proteins, this approach is questionable (Sankoff 2001; Wolfe 2001) and may have led to erroneous interpretations about both the number of events and their dates.”
Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat (2002, methodology): “…based on sequence similarity that did not intend to derive a consensus from the clusters (NCBI Uni-506 gene set, Schuler et al. , 1996), and (2) a competing methodology from TIGR that derived a high-quality consensus after applying very stringent clustering settings (Quackenbush et al. , 2000).”
Deep Proteomics of the Xenopus laevis Egg using an mRNA-derived Reference Database (2014, methodology): “laevisGene Indices version 11 [24, 46], and the de novo assemblies from the wild-type and J line RNA-seq data were combined (ensuring unique identifiers), cleaned and trimmed using SeqClean (http://compbio.”
miRU: an automated plant miRNA target prediction server (2005, background): “Currently, the system includes genome mRNAs or ESTs and other transcriptsassembled Gene Indices (13) for 28 plant species downloaded from The Institute for Genome Research (TIGR) at http:// www.”