With the ever increasing change and nature of the web, addresses may be out of date. In such a case, please inform the webmaster. In addition, this is in no way meant to be a comprehensive list of all databases and sites of importance. If you would like a site to be added, please email Dr Hamish S. Scott.

Mirror sites of many of the most important databases have been established and may provide faster local links. Last modified 15/11/2002


Databases

DNA and protein
GenBank at the National Library of Medicine / National Institutes of Health Search and retrieval site for all publicly available DNA sequences. Some tools for analyses and viewing
Genome Sequence DataBase GSDB at NCGR at the Los Alamos National Laboratory. Some tools for analyses and viewing
The EMBL Nucleotide Sequence Database Europe's primary nucleotide sequence resource. Some tools for analyses and viewing
DNA Data Bank of Japan The Japanese Equivalent of the above
DBCAT, The Public Catalog of Databases A list of most Molbiol/Genetic databases.

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Protein
 
ExPASy Molecular Biology Server*** Links to SWISSPROT and TrEMBL  (protein databases) and PROSITE (protein motif database) with functional annotations (proteomics tools).
Swissprot and TrEMBL SWISS-PROT is a curated protein sequence database while TrEMBL contains all the translations of EMBL nucleotide sequence entries not yet integrated in SWISS-PROT
Protein and associated topics databases Part of Amos's list
Protein 3D structure and associated topics databases Part of Amos's list

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Physical Maps,  Genetic Maps, Transcript Maps and Integration!
 
CHLC Cooperative Human Linkage Center DNA markers and Genetic maps.
An STS-Based Map of the Human Genome View or download physical and/or genetic maps at MIT.
Généthon Human Genome Research Centre Genetic and EST/STS maps.
CEPH Généthon Physical maps.
Marshfield Genetic Maps
The Genome Database Storage and curation of genomic mapping data.
Gene Map of the Human Genome, '98 ESTs and genes placed mainly by RH mapping
Gene Map of the Human Genome, '96

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SNP databases
 
HC21 cSNP database and map Chromosome specific cSNP database and map, covers a large proportion of chromosome 21 genes.
CHLC Cooperative Human Linkage Center CGAP Genetic Annotation Initiative, SNP collection.
Human SNP Database at MIT-WI Third Generation Genetic Map of the Human Genome (SNPs)
Single Nucleotide Polymorphisms in the Human Genome SNP database at Washington University, St. Louis 

Human Genic Bi-Allelic SEquences (HGBASE)

Human Genome Variation database (HGVbase)

A database of intra-genic (promoter to end of transcription) sequence polymorphism (SNPs).

The HGBASE database has adopted the new name HGVbase (Human Genome Variation database). This name change reflects the additional new role of the database as a central depository for mutation collection efforts undertaken in allegiance with the Human Genome Variation Society (HGVS).

A Database of Single Nucleotide Polymorphisms SNPs at NCBI

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Other Sequence Related Databases
 
REBASE NEBs comprehensive listing of nformation about restriction enzymes, methylases, and the microorganisms from which they have been isolated - isoschizomers, recognition sequences, cleavage sites, methylation specificity, commercial availability, and references - both published and unpublished.
Nucleotide and associated topics databases The world of nucleotides according to Amos

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Data retrieval tools
 
Search WWW Entrez at NCBI** NCBI's data retrieval tool, allows flexible seaching of NCBI databases simply to locate data or to create user specified data subsets in the required format. Old system.
Sequence Retrieval System*** EBI's data retreval tool, allows even more flexible seaching of any combination of local databases simply to locate data or to create user specified data subsets in the required format..

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Blast and Fasta Servers
 
Search DNA and Protein databases at NCBI with DNA or Protein with BLAST (Basic Local Alignment Search Tool) NCBI's sequence similarity search tool designed to support analysis of nucleotide and protein databases. Advanced BLAST page. BLAST 2 Sequences
GeneStream at the CRBM Blast and more at Montpellier
BLAST2.0 server at Swiss EMBnet Blast running at Swiss EMBnet node at SIB-ISREC in Lausanne. Now with a graphic and much faster!
FASTA searches (Similar to BLAST) FASTA searches at EBI
GeneMatcher Sequence searches by Smith-Waterman ISREC GeneMatcher, running at Swiss EMBnet node at SIB-ISREC in Lausanne. Faster and more sensitive than blast!
BLAST at HGMP BLAST at HGMP, registration required

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BioSoft to use on the NET

Catalogues, Where to go when you can't find it!
 
The UK MRC Human Genome Mapping Project Resource Center Comprehensive list of resources and services for scientists working on Genome Projects
Pedro's BioMolecular Research Tools Comprehensive list of resources, programs and services for scientists working in Molecular biology.
Baylor College of Medicine Search Launcher Molecular biology-related search and analysis services available on the WWW by function by providing a single point-of-entry for related searches
ExPASy Proteomics tools Protein identification and characterization, DNA -> Protein, Similarity searches, Pattern and profile searches, Primary structure analysis, Secondary structure prediction, Tertiary structure, Transmembrane regions detection, Sequence alignment
BioHunt search engine An automatically created database (by the Marvin molecular biology sites retrieval robot)
TIGEM catalogue Links to Bioinformatic Resources
TIGEM help! Documentation and manuals
The BioCatalog A software directory of general interest in molecular biology and genetics.
Where to go at EBI Network Navigation

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Tools

Tools for Analyses of Genomic Sequence
 
NIX - Introduction

Do an analysis

View your results!

A WWW tool to view the results of running many DNA analysis programs on your DNA sequence. 

The analysis programs run include: 

GRAIL, Fex, Hexon, MZEF, Genemark, Genefinder, FGene, BLAST (against many databases) Polyah, RepeatMasker,tRNAscan. Registration required

Gene identification tools A list of tools for gene identification
GAIA, Genomic sequence annotation at U.Penn An automated genomic sequence annotation system and its supporting database and vizualization tools.
The Genome Channel Automated annotation and graophical presentation of human genomic sequence

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EST Tools and databases
 
dbEST A division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or Expressed Sequence Tags.
Unique Gene Sequence Collection (UniGene), now for human's mice and rats.** Groupings of GenBank sequences that represent the transcription products of distinct genes.
German Genome project Blast of EST consensus sequences BLAST UniGene consensuses made by the German Genome project
EST Tools at TIGEM Directory of links to selected bioinformatic resources for Expressed Sequence Tags analysis
EST Blast Developed by Glaxo-Wellcome, running at the the UK MRC Human Genome Mapping Project Resource Center, registration required
WashU-Merck Human EST Project WashU and Merk EST data and tools. Traces. Trave viewing, etc
WashU-NCI CGAP EST Project As above but ESTs produced from CGAP
WashU-HHMI Mouse EST Project As above but for mouse ESTs
EMBL-EBI Traces and Clusters View EST clusters, alignments and traces
The IMAGE cDNA clone/library homepage Clones, sequences, libraries, vector information etc.
EST Scan A program to detect coding regions in DNA sequences, even if they are of 
low quality and correct sequencing errors that lead to frameshifts. At Swiss EMBnet node at SIB-ISREC in Lausanne. 

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Pairwise and Multiple Sequence Alignment Tools
 
 
BCM Search Launcher: Pairwise Sequence Alignment options You can all these searches from the BCM search launcher or go to the computer actually being used (linked)

SIM (Protein only, k best non-intersecting alignments) (EXPASY
ALIGN - optimal global alignment with no short-cuts (EERIE
LALIGN - calculates the N-best local alignments (EERIE
LFASTA - local similarity searches showing local alignments (EERIE)
BLAST 2 - local alignment using BLAST (NCBI
LAP2 - local DNA to protein alignment with LAP2 (MTU

The following servers return search results via Email: 
 PGWISE - comparisons of protein to genomic DNA (Pasteur)
 PCWISE - comparisons of protein to cDNA (Pasteur)

Protein Multiple Sequence Analysis links from HGMP Some of these may also be used for DNA
Multiple Sequence Analysis Menu from HGMP Registration required
BCM Search Launcher: Multiple Sequence Alignments You can all these searches from the BCM search launcher or go to the computer actually being used (if linked)

ClustalW 1.7 (DNA/Protein) - Global progressive 
CAP Sequence Assembly (DNA) - Contig Assembly Program 
MAP (DNA/Protein) - Global progressive in linear space
PIMA 1.4 (Protein only) - Pattern-Induced (local) Multiple Alignment 
MSA 2.1 (Protein only) - Near-optimal sum-of-pairs global (WashU)
BLOCK MAKER (Protein only) - Finds conserved blocks in seq sets (FHCRC)

The following server returns search results via Email:
ClustalW 1.7 (DNA/Protein) - Global progressive
MEME 2.2 (DNA/Protein) - Multiple EM for Motif Elicitation (SDSC)
Match-Box (Protein) - Blocks alignment with reliability 
    Registration required after 10 uses. (FUNDP)

Download GeneDoc A simple PC tool for shading alignments (mainly!)

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Proteomics Tools
 
ExPASy Proteomics tools Links to many online tools for analyses of proteins including translate, Protein identification and characterization, Pattern and profile searches, Primary structure analysis, Secondary structure prediction, Tertiary structure prediction, Transmembrane regions detection etc, 
ProfileScan Search a protein sequence or a short DNA sequence (frame-tolerant) against a profile database
PredictProtein PredictProtein retrieves similar sequences in the database and predicts aspects of protein structure.
PSORT Prediction of protein sorting signals and localization sites

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Miscellaneous  Tools
 
Repeatmasker at Universtiy of Washington, Seattle Filter sequences for known repeats (Alus, LTRs etc) and find simple repeats. A mirror site at  MGU,Harwell, UK
Primer3 at MIT Design primers for PCR, ASOs, etc. Best on the Net!
Webcutter Best webcutter site, most options (Rainbow, mutatgenesis etc). 
Readseq Convert between formats, complement etc, registration required
Readseq at BCM

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Chromosome 21 Sites, see also specific HC21 resource page
 
ERI Chromosome 21 Mapping and Sequence Database Links to HC21 sequence (Email BLAST server available), STS and Cell hybrid data
Index of protein sequence entries encoded on human chromosome 21 A lists of the human protein sequence entries whose genes are known to be encoded on chromosome 21 in the latest release of SWISS-PROT as maintained by Stylianos Antonarakis
Max Planck Institute for Molecular Genetics, Berlin, Germany Human Chromosome 21 Project in Berlin. Map display tool (Online Chromosome 21 Database), information about HC21 sequencing and HC21 Sequencing at MPIMG
Lawrence Berkeley National Laboratory Human Genome Center P1 map of the DSCR
Genome Sequencing Centre Jena German Genome project sequencing at Jena, including HC21, BLAST with no algnments, clone maps and Rummage analyses of sequence (follow the link to the appropriate map).
Dept. of Genome Analysis, GBF Braunschweig German Genome project sequencing at GBF Braunschweig, including HC21
Japanese Genomic Sequencing The ALIS Project in JST encourages large-scale DNA sequencing Projects in Japan. Sequencing data and maps, including HC21, from either the Department of Molecular Biology,  Keio University School of Medicine,  including maps or the Human Genome Center,  Institute of Medical Science,  University of Tokyo (see Chromosome 21 Sequence Maps below), is available here.
Human Chromosome 21 Sequence Map Institute of Medical Science, The University of Tokyo, Human Genome Research Group, Genomic Sciences Center at RIKEN and Human Genome Center with BLAST
Integrated Human Chromosome 21 Maps with Sequence Human Genome Research Group, RIKEN Genomic Sciences Center (GSC) with Integrated Marker Arrangement Project
UniGene data on HC21 Known and unknown HC21 transcripts as represented mainly by ESTs
Gene Map of the Human Genome, '98 HC21 Known and Genes and Unigene clusters that map to HC21 by RH mapping (Can be some errors)
Whitehead Institute/MIT Center for Genome Research Genetic (including SNP), physical, STS, Radiation hybrid and integrated maps of the human genomeHC21 SNPs
Partial aneuploidies of chromosome 21: a genotype and phenotype database. This database can be accessed through the infobiogen server with a password obtained from J.Delabar :delabar@necker.fr
HC21 SNPs produced in Geneva 12/20 genes tested posted so far (25/4/99)! Follow the link and ask  Dr Hamish S. Scott for additional information. Password protected. More genes and SNPs from genomic sequence coming soon
CEPH Chromosome 21 mapping resources Some information on BACs, STSs etc
NCBIs Human Genome Resources Guide Including their guide to HC21 genomic sequencing
List if HUGO/GDB Chromosome Editors, including HC21
See also Down syndrome sites

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Genome Centres and Sequencing Centres
 
The Institute of Genome Research (TIGR) Craig Venter's old company/ Institute
Whitehead Institute/MIT Center for Genome Research Genetic (including SNP), physical, STS, Radiation hybrid and integrated maps of the human genome
Australian Genome Research Facility Services for sequencing, genotyping and mutation analyses at great prices!
Infobiogen  
The Sanger Centre  
Généthon  
Baylor College of Medicine Human Genome Sequencing Center  
Lawrence Berkeley National Laboratory Human Genome Sequencing Department  
Lawrence Livemore National Laboratory Human Genome Center  
Stanford Human Genome Center  
Washington University Center for Genetics in Medicine  
Genome Sequencing Center, Washington University, St. Louis ESTs, human genomic sequence etc, Washington University, St. Louis
Department of Molecular Biotechnology, University of Washington, Seattle  Lee Hood
University of Texas Southwestern Medical Genome Science and Technology Center  
The Human Genome Sequencing Index (HGSI) A site to support coordination and tracking of sequencing of Human chromosomes
Celera Craig Venter and Perkin Elmers new baby. Watch for Drosophila, mouse and human genomic sequences!
University of Washington Genome Center, Seattle Maynard Olson

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Sites of General Interest to the Human Genome Project
 
U.S. Department of Energy - Human Genome Project Information Information about the history, progress, research, and resources of the Human Genome Project.
US National Centre for Human Genome Research As above.
The Human Genome Organisation Describes the International co-ordination role of HUGO in the HGP.

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Searchable Links of Genetic for Genetics Related Sites
 
GeneNet A comprehensive, interactive network on the Internet for the field of genetics
GeneCards: integrating information about gene functions and biomedical applications A database of human genes, their products and their involvement in diseases.

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Genetic Disease Databases
 
Online Mendelian Inheritance in Man - OMIM Home Page A catalogue of human genes and genetic disorders. Search OMIM
The Human Gene Mutation Database A collation of the majority of known (published) gene lesions responsible for human inherited disease.

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Differential Gene Expression Sites
 
SAGE home page Homepage of Kinzler and Vogelsteins SAGE 
Gene Chips DNA Microarrays
Cancer Genome Anatomy Project SAGE The NCIs SAGE data and tools page for cancer SAGE
Genzyme Molecular Oncology Holders of the SAGE patent, offering services and performing their own studies. 
Cancer Genome Anatomy Emerging Technologies A list of laboratories and companies interested and developing high throughput DGE Techniques such as microarrays
Large-Scale Gene Expression and Microarray Links and Resources A collection of web resources and pointers to information on large-scale gene expression studies, and especially microarray technologies.

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Journals and Publishers
 
PubMed, Medline searches Searching Medline. Old system.
CMU library Search for titles held and on line subscriptions
Alternative Medline at BioMedNet Some good download options. Slightly behind PubMed.  Registration required
Alternative Medline at COS Community of Science Medline
Amos' WWW links page A list of journals and publishers
Cell
Science
Nature
Nature Genetics
The American Journal of Human Genetics
Human Molecular Genetics
Genome Research
Human Genetics
Genomics
Unrestricted access to Trends Journals (reviews)  TIBS, TIGS, Immunology Today etc
Full-Text of more than a hundred journals
Expasy's list A comprehensive list of biological journals, publishers and web sites.
Passwords for Members of Medical Genetics Yes, this is password protected too!

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Model Organism Databases
 
Mouse Genome Database Links to genetic, physical and homology maps in mice
Drosophila Genome database (Flybase) Genetic and molecular data for Drosophila
The C. elegans Genome Project Links to C.elegans sequences,and other genetic information
The Saccharomyces Genome Database (SGD) A variety of genomic and biological information on yeast.
E. coli Genome Center's Home Page Sequence and map data from E. coli.
Amos's links to organism specific databases Plants, animals, bacteria, even human chromosomes count as organisms!

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Societies and Miscellaneous
 
The American  Society of  Human  Genetics
The European Society of Human Genetics
Amos's List of Biological Societies and Organizations
Human gene nomenclature homepage Check you gene name, ask for a gene name, standard nomenclature for gene families
World Wide Web Consortium Home of the web!
BIOSCI/bionet Electronic Newsgroup Network for Biology Newsgroups  intended primarily for communications between researchers

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Supplies and Ordering
 
BioSupplyNet Where to find biomedical research supplies (chemicals, biologicals, instruments) and suppliers
Microsynth Our current oligonucleotide provider
Order cell lines, probes or other biologicals, list at HGMP Many organisations make collections of biological material available. These are pages that provide online databases of their collections. 

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Search Engines
 
All the Web
Altavista
Excite
Google
HotBot
Infoseek
LookSmart
Lycos
Metacrawler
NetScape
Yahoo!

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