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Transitioning from LocusLink to Entrez Gene
Cancer Chromosomes: a New Entrez Database
HomoloGene: An Entrez Database with a New Look
BLAST Link (BLink) to Protein Alignments and Structures
Debut of the HCT Database and Anthropology/Allele Frequencies in dbMHC
350kb Sequence Length Limit Removed by Sequence Database Collaboration
New Eukaryotic Genomes at NCBI
Environmental Samples Make Big Splash
HIV Protein-Interaction Database
e-PCR and Reverse e-PCR: Greater Sensitivity, More Options
New Organisms in UniGene
RefSeq Accession Numbers Get Longer as Rat Gets Last 6-digit Accession
Slots available for FieldGuidePlus Training Course Onsite at NCBI
RefSeq Release 6 on FTP Site
Exponential Growth of GenBank Continues with Release 142
Entrez Tools is a 'Hot Spot'
BLAST Lab: Using BLASTClust
New Microbial Genomes in GenBank
Entrez Quiz
Masthead
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HomoloGene: An Entrez Database with a New Look
HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes. The genomes represented in the recent Build 36 of HomoloGene include H. sapiens, M.musculus, R.norvegicus , D. melanogaster , A. gambiae, C. elegans , S. pombe, S. cerevisiae , N. crassa, M. grisea, A. thaliana, and P. falciparum.
NCBI has adopted a new Homolo-Gene build procedure which is guided by the taxonomic tree, relies on conserved gene order and measures of DNA similarity among closely related species, while making use of protein similarity for more distantly related organisms. The new computational procedure greatly increases the reliability of the computed homologous gene sets and the resulting HomoloGene entries now include paralogs in addition to orthologs. For more details or to search the database, see the Homologene home page at:
New Search Strategies Supported
Because HomoloGene is now an Entrez database, it can be queried using an assortment of fielded terms combined with boolean operators. Among the fields unique to Homolo-Gene is the “Ancestor” field which refers to the taxonomic group of the last common ancestor of the species represented in a HomoloGene entry. Using the “Ancestor” field it is possible to limit a search to genes conserved in one of 9 ancestral groups: Sordariomycetes (147,550 entries), Eukaryota (2,759 entries), Fungi/Metazoa (33,154 entries), Bilateria (33,213 entries), Coelomata (33,316 entries), Mammalia (9,172 entries), Ascomycota (1,083 entries), Insecta (1,689 entries), Rodentia (1,587 entries).
New Views of the Data
HomoloGene reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man (OMIM), Mouse Genome Informatics (MGI), Zebrafish Information Network (ZFIN), Saccharomyces Genome Database (SGD), Clusters of Orthologous Groups (COG), and FlyBase. A “Pairwise Scores” display gives a table of pairwise statistics for members of a Homologene group that includes percent amino acid and nucleotide identities, the Jukes-Cantor genetic distance parameter (D), the ratio of non-synonymous to synonymous amino acid substitutions (Ka/Ks) for predicted proteins, and the ratio of radical to conservative changes in the transcript (Knr/Knc).
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