Genetics databases
From MyBio
Also see Genomics databases
[edit] Categories which link here
[edit] Genetics databases - Quick Links
| ALFRED | MethDB | |
| ACLAME | DEG | |
| POLYGENIC PATHWAYS |
[edit] Genetics databases - Web Resources
ALFRED ALelle FREquency Database. ALFRED (the ALelle FREquency Database) is designed to store and disseminate frequencies of alleles at human autosomal polymorphic sites for multiple defined population samples, primarily for the population genetics and molecular anthropology communities. The focus is on allele frequencies of normal, common DNA variants, i.e., polymorphisms, in samples of anthropologically defined populations. Links are provided to molecular databases for precise definitions and locations of the polymorphisms and to anthropologic databases for linguistic, ethnographic, and demographic information on the populations sampled. References to publications are associated with the frequencies and linked to PubMed whenever possible. Many polymorphisms have linkes to low-tech protocols suitable for small laboratories engaged in anthropologic research. ALFRED has information on 672 polymorphic sites typed on at least one population sample and 288 populations typed for at least one polymorphism.
MethDB
DNA methylation data, patterns and profiles. MethDB is a public database for DNA methylation. This constantly growing data base has become a key resource in the field of DNA methylation research. The database contains currently methylation patterns, profiles and total methylation content data for 46 species, 160 tissues and 72 phenotypes coming from a total of 6667 experiments (as of 4/9/2002). These data can be conviniently searched and represented in different ways. Recently, we have included an on-line submission tool that permits the scientific public to directly enter data into MethDB.
| DPL Forum: Too few categories! |
ACLAME
A CLAssification of Mobile genetic Elements. The ACLAME database is a collection and classification of prokaryotic mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to providing information on the full genomes and genetic entities, it aims to build a comprehensive classification of the functional modules of MGEs at the protein, gene and higher levels. This first version contains a comprehensive classification of 5069 proteins from 119 DNA bacteriophages into over 400 functional families. This classification was produced automatically using TRIBE-MCL, a graph-theory-based Markov clustering algorithm that uses sequence measures as input, and then manually curated. Manual curation was aided by consulting annotations available in public databases retrieved through additional sequence similarity searches using Psi-Blast and Hidden Markov Models. The database is publicly accessible and open to expert volunteers willing to participate in its curation. Its web interface allows browsin as well as querying the classification. The main objectives are to collect and organize in a rational way the complexity inherent to MGEs, to extend and improve the inadequate annotation currently associated with MGEs and to screen known genomes for the validation and discovery of new MGEs.
DEG Database of essential genes. Essential genes are genes that are indispensable to support cellular life. These genes constitute a minimal gene set required for a living cell. We have constructed a Database of Essential Genes (DEG), which contains all the essential genes that are currently available. The functions encoded by essential genes are considered a foundation of life and therefore are likely to be common to all cells. Users can BLAST the query sequences against DEG. If homologous genes are found, it is possible that the queried genes are also essential. Users can search for essential genes by their function or name. Users can also browse and extract all the records in DEG. Essential gene products comprise excellent targets for antibacterial drugs. Analysis of essential genes could help to answer the question of what are the basic functions necessary to support cellular life.
POLYGENIC PATHWAYS
A database of genes and risk factors implicated in Alzheimer's disease, Bipolar disorder or Schizophrenia
