The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species

By John Quackenbush, Jennifer Cho, Daniel Lee, F. Liang, I. Holt, S. Karamycheva, Babak Parvizi, Geo Pertea, R. Sultana, Joseph White. Nucleic Acids Res., 2001

506 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cc1efeb4d46224afb4e55bbd15c98184d03f6383

How researchers see this paper

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

In Genetics

In Molecular Biology

Citations in the corpus

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. (2003, methodology): “These transcript alignment assembly-based gene structure annotation updates were performed as part of the TIGR complete Arabidopsis genome re-annotation effort (20).”
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets (2003, methodology): “TGICL is used to generate the TIGR Gene Indices (TGI; Quackenbush et al., 2001; http://www.tigr.org/tdb/tgi/), representing independent analyses for nearly 60 species with EST collections of fewer than 10 000 to more than 4 000 000 sequences.”
Gene silencing in plants using artificial microRNAs and other small RNAs. (2008, background): “All 34 EST libraries currently found in the Gene Index Project (Quackenbush et al., 2001; http://compbio.dfci.harvard.edu/tgi/plant.html), including those from maize, tobacco and soybean, have been integrated into WMD for amiRNA predictions.”
Predicting the Conditional Probability of Discovering a New Class (2004, background): “We studied a genomic dataset concerning a cDNA library made from the 0- to 3-mm buds of tomato flowers (Mao and Lindsay 2002; Quackenbush, Cho, and Lee 2000).”
The TIGR Rice Genome Annotation Resource: improvements and new features (2006, methodology): “Thus, the TIGR Gene Indices contain non-experimentally based sequences and are a possible source of annotation error propagation.”
OrthoMCL: identification of ortholog groups for eukaryotic genomes. (2003, methodology): “…bias), and when i = j, to minimize the impact of “recent” paralogs (duplication within a given species) on the clustering of cross-species orthologs (Quackenbush et al. 2000, 2001) Gene indices are then used to construct ortholog groups by pairwise comparisons, using an approach similar to that…”