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Clusters of Orthologous Groups
[NCBI] (COGs) A phylogenetic database (with a comparison search server incorporated) of orthologous proteins in many complete genomes.
Gene OntologyTM Consortium
The goal of the Gene OntologyTM Consortium is to produce a dynamic controlled vocabulary
that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
GenomePixelizer – Genome Visualization Tool
[University of California at Davis] GenomePixelizer was designed to help in visualizing the relationships between duplicated genes in genome(s) and to follow relationships between members of gene clusters. GenomePixelizer may be useful in detection of duplication events in genomes, tracking the “footprints” of evolution, as well as in displaying the genetic maps and other aspects of comparative genetics.
Gramene: A Comparative Mapping Resource for Grains
Gramene was recently funded by the USDA IFAFS programme to create a curated, open-source,
Web-accessible data resource for comparative genome analysis in the grasses. Our goal is to
facilitate the study of cross-species homology relationships using information derived from public
projects involved in genomic and EST sequencing, protein structure and function analysis, genetic
and physical mapping, interpretation of biochemical pathways, gene and QTL localization and
descriptions of phenotypic characters and mutations.
Human-Mouse Homology Map
[NCBI] The Human-Mouse conserved synteny maps are now being computed using
a variety of inputs. Currently, there are two human genome assemblies, the
UCSC genome assembly and the NCBI genome assembly. In addition, we
are using two sources of mouse mapping data, the MGD map, and the
Whitehead/MRC Radiation Hybrid map. These various maps can be
compared to produce slightly different overviews of conserved synteny
between humans and mice.
Kyoto Encyclopedia of Genes and Genomes
[GenomeNet] “KEGG is an effort to computerize current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes and to provide links from the gene
catalogs produced by genome sequencing projects.”
Links to Pathway and Other Databases
[GenomeNet] A comprehensive list of links to biological and biochemical databases. The types of databases include: metabolic pathways; enzymes, compounds, and elements; regulatory pathways; protein-protein interactions; nomenclature and classification; taxonomy; and complete genomes and analysis.
Mammalian Homology and Comparative Maps
[Mouse Genome Informatics] (The jackson Laboratory) MGD contains homology information for mouse, human and 15 other mammalian species. Most of the information for homologies
is extracted from the published scientific literature. In general, these papers explicitly report homology relationships and MGD
reflects that published information.
Ortholog/Paralog Groups of Functional Units
[Institute for Chemical Research, Kyoto University] Conserved gene clusters in the KEGG metabolic and regulatory pathways.
[Munich Information Center for Protein Sequences] (Protein Extraction, Description, and ANalysis Tool) “PEDANT is a software system for completely automatic and exhaustive analysis of protein sequence sets – from individual sequences to complete genomes.”
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Proteome Analysis @ EBI
[EBI] The Proteome Analysis database has been set up to provide comprehensive statistical and comparative analyses of the predicted proteomes of fully sequenced organisms. The analysis is compiled using InterPro, CluSTr and GO, and is performed on the non-redundant complete proteome sets of SWISS-PROT and TrEMBL entries.