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Genome Central
OMIM (Online Mendelian Inheritance in Man)
GDB (Genome DataBase)
GeneCards - integrated biomedical genetic information
The Unified Database for Human Genome Mapping
OMIM gene map
EnsEMBL - annotated human sequences
The HuGeMap database
GenAtlas
Genome Navigator: Whitehead/MIT STS-based Map of the Human Genome
The Genome Channel
Whitehead/MIT STS-Based Map of the Human Genome
Transcript Map of the Human Genome
Human Telomere Information
The Genetic Location Database (LDB)
The dysmorphic human and mouse homology database
BodyMap - Anatomical Expression Database of Human Genes
CEPH-Genethon integrated map
CEPH Genotype database
Cooperative Human Linkage Center (CHLC)
GeneMap '98 - The International RH Mapping Consortium Map
Radiation Hybrid Mapping data (RHdb)
dbEST Expressed Sequence Tag Database
UniGene - Unique Human Gene Sequence Collection
dbSTS Sequence Tagged Site Database
Whitehead Institute/MIT Genome Center
V BASE: A Directory of Human Immunoglobulin V Genes
Human CpG Island database
Human population genetics database (Genography)
Anthony Nolan Research Institute (ANRI)
GDB Nomenclature Committee
Atlas of Genetics and Cytogenetics in Oncology and Haematology
Human Genome - The Third Millennium
Human BAC Fingerprint Database
Genome Central
In the context of the completion of the"Working Draft" of the Human
Genome Sequence by the public Human Genome Project, here are some URLs
that are good starting points for working with the data.
The vast majority of the human genome is now publicly available. About 25% of the genome is in finished form, while the great majority of the remainder is in draft form. A publication on the working draft will be submitted later this year.
As with other organisms, the full primary source data is available in each of three public databases: Genbank, EMBL and DDBJ. The information is being searched and analyzed by tens of thousands of scientists in academia and industry.
Still, it is a daunting and time-consuming task for users to directly analyze the primary source data. Many users would like access to ancillary information and tools that provide an ongoing picture of the genome that is both comprehensive and comprehensible. Such information includes the overlaps between clones; the correct genomic location of each clone; an integrated genomic sequence that merges the individual clones; and annotation of gene content.
In fact, such resources have been developed and are freely available - but they are not widely known.
For ease of access, we have created a master web site called"Human Genome Central" containing a brief listing of links to some of the most useful public resources; further links to additional sites can be found within them. The web sites will be regularly updated with new information.
OMIM (Online Mendelian Inheritance in Man)
This database is a catalog of human genes and genetic disorders authored
and edited by Dr. Victor A. McKusick and colleagues at NCBI, Bethesda,
Maryland.
GDB (Genome DataBase)
GDB holds data on Human gene loci, polymorphisms, mutations, probes, genetic
maps, GenBank, citations and contacts.
GeneCards - integrated biomedical genetic information
Although it will take some years until the human genome is totally
sequenced, and still a much longer time to learn about the functions of
the products of those genes, the complex organization and the vast
amount of biomedical information already accessible often cause certain
problems that are somehow connected to the phenomenon of"information
overflow" and the often very time-consuming process of information
retrieval or mining. Thus, many scientists feel that new approaches to
organize scientific information are urgently needed.
GeneCards is a database that intends to address some of these problems by integrating biomedical information taken from several sources (GDB, MGD, OMIM, SWISS-PROT, HGMD, Doctor's Guide to the Internet), and by presenting them in a way facilitating a quick.
The Unified Database for Human Genome Mapping
The Unified Database (UDB) integrates information on the human genome,
with emphasis on mapping information. Mapped DNA segments, classified
by categories (such as genes, EST clusters and STSs mapped by various
methods) are presented on a Megabase-scale integrated map, with further
information and links to relevant databases.
UDB includes data from numerous resources, including the Genome Database, Whitehead Institute/MIT Center for Genome Research, Genethon, GeneMap'99 and others. Integrated map locations were calculated from separate method-specific chromosome maps (e.g. genetic linkage, radiation hybrid, and content-contig maps) by a simple scaling algorithm.
OMIM gene map
The OMIM gene map presents the cytogenetic map location of disease genes and other
expressed genes described in OMIM.
You enter a position, say '17q11' and you get all the omim records in that regionn, even things that map to '17cen-q12'
EnsEMBL - annotated human sequences
Ensembl is a joint project between EMBL-EBI and the Sanger Centre to
develop a software system for automating analysis of genomic data. It
is being applied to the publically released human genome data stream.
The HuGeMap database
HuGeMap is a database that contains:
GenAtlas
Compiles the information relevant to the mapping efforts of
the Human Genome Project.
GENATLAS/GEN is a repertory of three types of objects : genes, diseases, and markers.
Genome Navigator: Whitehead/MIT STS-based Map of the Human Genome
Genome Navigator is an attempt to provide a visual interactive gateway
to major databases containing physical and genetic mapping information
about the human genome.
Genomic maps of these organisms are displayed using DerBrowser, a Java applet, designed as a universal tool to display and navigate various types of maps. Among other features, it allows a user to query external databases about any map object.
The Genome Channel
This system is a prototype graphical browser for querying the annotated
reference genome.
The Java interface relies on a number of underlying resources, analysis tools and data-retrieval agents to provide an up-to-date view of genomic sequences as well as computational and experimental annotation. Designed to be simple enough for a layperson, the channel also offers sophisticated capabilities for hypothesis testing.
Whitehead/MIT STS-Based Map of the Human Genome
This contains YAC screening data for several thousand STSs. For each
STS, information is held on the following types of raw data (where available):
Transcript Map of the Human Genome
A small portion of each cDNA sequence is all that is needed to develop
unique gene markers, known as sequence tagged sites or STSs, which can
be detected in chromosomal DNA by assays based on the polymerase chain
reaction (PCR). To construct a transcript map, cDNA sequences from a
master catalog of human genes were distributed to mapping laboratories
in North America, Europe, and Japan. These cDNAs were converted to STSs
and their physical locations on chromosomes determined on one of two
radiation hybrid (RH) panels or a yeast artificial chromosome (YAC)
library containing human genomic DNA. This mapping data was integrated
relative to the human genetic map and then cross-referenced to
cytogenetic band maps of the chromosomes. (Further details are
available in the accompanying article in the 25 October issue of
SCIENCE).
The histograms reflect the distributions and densities of genes along the chromosomes. Because the individual genes (>16,000) are too numerous to represent, images have been chosen to illustrate the myriad aspects of human biology, pathology, and relationships with other organisms that can be revealed by analysis of genes and their protein products.
Human Telomere Information
This is a section of GenLink's Teldb giving literature citations and
other information on human telomeric regions.
The Genetic Location Database (LDB)
Ldb is an analytical database for constructing fully integrated genetic and physical maps. The ldb
program generates an integrated map (known as the summary map) from partial maps of physical,
genetic, regional, somatic hybrid, mouse homology and cytogenetic data.
The summary maps and the data used to build up such maps are available from this site. The files for each chromosome are stored in the same directory which include the summary map, partial maps, lod files and the parameter files. As this server is experimental many of the chromosome directories are incomplete with the most complete map sets being chromosomes 1,9,21 and X.
The dysmorphic human and mouse homology database
This consists of three separate databases of human and mouse
malformation syndromes together with a database of mouse/human syntenic
regions. The mouse and human malformation databases are linked together
through the chromosome synteny database. The purpose of the system is
to allow retrieval of syndromes according to detailed phenotypic
descriptions and to be able to carry out homology searches for the
purpose of gene mapping. Thus the database can be used to search for
human or mouse malformation syndromes in different ways:-
BodyMap - Anatomical Expression Database of Human Genes
BodyMap is a data bank of expression information of human genes, novel
or known, in various tissues or cell types. It is created by random
sequencing of clones in 3'-directed cDNA libraries. Since these clones
were not amplified, redundancy of the same sequence reflects the
quantitative aspect of gene expression in various tissues.
You can enter your sequence and it will be matched using fasta to the cDNA sequences in this database.
CEPH-Genethon integrated map
This page allows you to search the CEPH-Genethon mapping data used to
build the first generation physical map of the human genome. It gives
information on the CEPH YAC library and the QUICKMAP database with the
infoclone program to get information about a STS or a YAC.
CEPH Genotype database
The Centre d'Etude du Polymorphisme Humain (CEPH) maintains a database of genotypes for all
genetic markers that have been tested in the reference families for linkage mapping of the human
chromosomes.
Cooperative Human Linkage Center (CHLC)
The goal of the Cooperative Human Linkage Center is to develop
statistically rigorous, high heterozygosity genetic maps of the human
genome that are greatly enriched for the presence of easy-to-use
PCR-formatted microsatellite markers.
GeneMap '98 - The International RH Mapping Consortium Map
This is the latest Radiation Hybrid Consortium Human map.
Radiation Hybrid Mapping data (RHdb)
Radiation hybrid maps are an indispensable alternative to genetic
maps as they can include non-polymorphic markers and are also
powerful enough to order unresolved genetic clusters of polymorphic
STSs. An international collaborative project has been started
which will produce a large number of these hybrids for the human genome.
This in turn will allow the generation of a very precise STS map that
will be indispensable in the study of multifactorial diseases.
RHdb, the radiation hybrid database is an archive of raw data with links to other related databases. The main data is stored in a relational database. Submissions to this database are made using a standard format. Various export formats will be supported, as well as different ways of accessing the data.
dbEST Expressed Sequence Tag Database
The dbEST Database holds many Human ESTs.
UniGene - Unique Human Gene Sequence Collection
This holds clusters of human EST sequences that represent
the transcription products of distinct genes.
These sequences are being used for transcript mapping in collaboration with several genome mapping centers. Some of the clusters have already been localized to chromosomes, but more detailed mapping map information is not available at this time.
dbSTS Sequence Tagged Site Database
The dbSTS Database holds many Human STSs.
Whitehead Institute/MIT Genome Center
V BASE: A Directory of Human Immunoglobulin V Genes
A directory of human immunoglobulin germline variable region sequences
compiled from over a thousand published sequences (including those in
the current releases of the Genbank and EMBL data libraries). There are
seven directories: D, JH, JK, JL, VH, VK and VL. Each directory
consists of a folder or file containing the germline sequences and a
file containing the corresponding reference list.
Human CpG Island database
Look at the Human CpG Island database. This is a flat file containing a
description of genes and their associated CpG islands.
Human population genetics database (Genography)
A database of human genetic and cultural
diversity, to act as a comprehensive community repository
supporting work in human population genetics and quantitative
anthropology.
The currently available version of the database contains 100,000 gene frequencies from almost 2,000 populations, collected from the literature on classical polymorphisms (essentially protein data) published up to 1986. These data were used for calculations on which the book History and Geography of Human Genes, by Cavalli-Sforza, Menozzi, and Piazza, is based.
Future versions of the database will include an update of the classical polymorphism data, a collection of published and unpublished DNA data by individual and by population (including RFLPs, microsatellites, and SNPs), and the future CEPH database, to be collected in collaboration with the Human Genome Diversity Project. In addition, information about geography, regional ecology, linguistics, mythology, musicology, and physical anthropology will be included. Finally, various analysis and visualization tools will be provided.
Anthony Nolan Research Institute (ANRI)
The WHO Nomenclature and HLA Sequence alignments are available from this site,
together with monthly updates.
Atlas of Genetics and Cytogenetics in Oncology and Haematology
The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a
cooperative process of reviewing and updating on somatic genetics,
clinical entities in cancer, and on cancer-prone diseases; it is made
for and by: cytogeneticists, molecular biologists, and geneticists in
general, clinicians in oncology and in haematology, and pathologists.
Human Genome - The Third Millennium
This site aims to help researchers find their way in Web-accessible
databases containing Human Genome information, and to find answers to
problems related to human genomic clones, contigs, sequences and maps.
It contains:
Human BAC Fingerprint Database
The Human fingerprint database consists of fingerprints generated at the
GSC from various Human libraries. Approximately 268K fingerprints were
generated from the RPCI-11 BAC library and are designated with an"N" in
the on-line search and in the FPC database. We are currently
fingerprinting other BAC libraries for the Human fingerprint database.
These are BACs from the Caltech library B,C and D1 are designated with
an"M" and RPCI-13 BACs are designated with an"F". All other
fingerprints that are available from the database were generated in
collaboration with other labs.
Any Comments, Questions? Support@hgmp.mrc.ac.uk