Comparative genomics promises to rapidly accelerate the identification and functional classification of biologically important human genes. We developed the TIGR Orthologous Gene Alignment (TOGA; ) database to provide a cross-reference between fully and partially sequenced eukaryotic transcribed sequences. Starting with the assembled expressed sequence tag (EST) and gene sequences that comprise the 28 TIGR Gene Indices, we used high-stringency pair-wise sequence searches and a reflexive, transitive closure process to associate sequence-specific best hits, generating 32,652 tentative ortholog groups (TOGs). This has allowed us to identify putative orthologs and paralogs for known genes, as well as those that exist only as uncharacterized ESTs and to provide links to additional information including genome sequence and mapping data. TOGA provides an important new resource for the analysis of gene function in eukaryotes. In addition, an analysis of the most widely represented sequences can begin to provide insight into eukaryotic biological processes.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC155294PMC
http://dx.doi.org/10.1101/gr.212002DOI Listing

Publication Analysis

Top Keywords

tigr orthologous
8
orthologous gene
8
gene
5
cross-referencing eukaryotic
4
eukaryotic genomes
4
genomes tigr
4
gene alignments
4
alignments toga
4
toga comparative
4
comparative genomics
4

Similar Publications

Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes.

Nucleic Acids Res

January 2021

Sorbonne Université & CNRS, UMR 7144 'Adaptation & Diversity in the Marine Environment' (AD2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France.

Cyanorak v2.1 (http://www.sb-roscoff.

View Article and Find Full Text PDF
Article Synopsis
  • Camellia oleifera is a key tree species in China known for producing edible oils rich in unsaturated fatty acids, drawing significant interest for its health benefits.
  • The study involved analyzing the transcriptome and proteome of C. oleifera seeds from Hainan Island, employing techniques like RNA-seq and mass spectrometry to identify numerous transcripts and protein species.
  • Key findings revealed many unigenes and proteins involved in lipid metabolism, highlighting specific proteins' roles in fatty acid breakdown, and suggesting potential applications in enhancing oil regulation for this crop.
View Article and Find Full Text PDF

Trichomonas vaginalis causes the trichomoniasis, in women and urethritis and prostate cancer in men. Its genome draft published by TIGR in 2007 presents many unusual genomic and biochemical features like, exceptionally large genome size, the presence of hydrogenosome, gene duplication, lateral gene transfer mechanism and the presence of miRNA. To understand some of genomic features we have performed a comparative analysis of metabolic pathways of the T.

View Article and Find Full Text PDF

Identification and validation of reference genes for quantitative RT-PCR normalization in wheat.

BMC Mol Biol

February 2009

Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, Via S. Camillo de Lellis, 01100 Viterbo, Italy.

Background: Usually the reference genes used in gene expression analysis have been chosen for their known or suspected housekeeping roles, however the variation observed in most of them hinders their effective use. The assessed lack of validated reference genes emphasizes the importance of a systematic study for their identification. For selecting candidate reference genes we have developed a simple in silico method based on the data publicly available in the wheat databases Unigene and TIGR.

View Article and Find Full Text PDF

A molecular phylogenomic analysis of the ILR1-like family of IAA amidohydrolase genes.

Comp Funct Genomics

June 2010

Montclair State University, Department of Biology and Molecular Biology, 1 Normal Avenue, Montclair, NJ 07043, USA.

The ILR1-like family of hydrolase genes was initially isolated in Arabidopsis thaliana and is thought to help regulate levels of free indole-3-acetic-acid.We have investigated how this family has evolved in dicotyledon, monocotyledon and gymnosperm species by employing the GenBank and TIGR databases to retrieve orthologous genes. The relationships among these sequences were assessed employing phylogenomic analyses to examine molecular evolution and phylogeny.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!