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Important Home Pages
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European Molecular Biology Laboratory (EMBL)
http://www.ebi.ac.uk/ebi_docs/embl_db/ebi/topembl.html
Cambridge, UK.

UK Human Genome Mapping Project - Resource Center (HGMP-RC)
http://www.hgmp.mrc.ac.uk/

SeqNet: UK Node of European Molecular Biology Network (EMBNet)
http://www.seqnet.dl.ac.uk/

GenBank
http://www.ncbi.nlm.nih.gov/Web/Search/index.html
GenBank at the National Center for Biotechnology (NCBI) of The National Library of Medicine (NLM) at The National Institutes for Health (NIH) campus, USA.

DNA Databank of Japan (DDBJ)
http://www.ddbj.nig.ac.jp

Genome Sequence DataBase (GSDB)
http://seqsim.ncgr.org/
The National Center for Genome Resources, Genome Sequence Database.
The server is a supercomputer with genomic algorithm accelleration.

Online Mendelian Inheritance in Man (OMIM)
http://www3.ncbi.nlm.nih.gov/Omim/searchomim.html
Database of human genes and their disorders, with textual information, images and references. Links to Entrez and MedLine.

European Drosophila Genome Project
http://edgp.ebi.ac.uk/

The Institute for Genomic Research (TIGR)
http://www.tigr.org/

The Sanger Centre
http://www.sanger.ac.uk/

Swiss Institute of Bioinformatics (Expasy)
http://www.expasy.ch/

GenomeNet (Japan)
http://www.genome.ad.jp/

Australian National Genomic Information Service (ANGIS)
http://morgan.angis.su.oz.au

Bioinformatics and Biology Resources on the Internet
http://aeiveos.wa.com/biology/index.html
An excellent site, well worth a visit!

List of other Genome Sites
http://www.hgmp.mrc.ac.uk/GenomeWeb/
List of other genome web sites. Concise and clearly presented.

Brunel University Online Teaching Programme
http://www.brunel.ac.uk/depts/bl/project/front.htm
Manuals
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EMBL
http://www.ebi.ac.uk/ebi_docs/embl_db/usrman/usrman.html

GenBank
ftp://ncbi.nlm.nih.gov/genbank/gbrel.txt

SRS
http://www.sanger.ac.uk/srs/srsman.html
Other Guides and Tutorials
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BioComputing Hypertext Coursebook
http://www.techfak.uni-bielefeld.de/bcd/Curric/
A very thorough source of learning. Especially good for readers who want to get to grips with the "nuts and bolts" of bioinformatics.
Molecular Genetic Information
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Gene Cards (*)
http://bioinfo.weizmann.ac.il/cards/
A very useful site providing comprehensive information and links. Direct links to GenBank, SWISS-PROT and MedLine. Includes synonyms, similar genes in other organisms, gene products and details about disorders.

Gene Cards: Diseases with a Genetic Association (*)
http://bioinfo.weizmann.ac.il/cards-bin/listdiseasecards http://bioinfo.weizmann.ac.il/cards/cards-bin/listdiseasecards
View the complete (comprehensive!) list, or search for disease related genes by chromosome.

Life Science Dictionary
http://biotech.chem.indiana.edu/pages/dictionary.html
A dictionary.
Genomic Sequence Databases
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These are the four primary sequence databases. They exchange sequence information daily.
European Molecular Biology Laboratory (EMBL)
http://www.ebi.ac.uk/ebi_docs/embl_db/ebi/topembl.html
Cambridge, UK.

GenBank
http://www.ncbi.nlm.nih.gov/Web/Search/index.html
GenBank at the National Center for Biotechnology (NCBI) of The National Library of Medicine (NLM) at The National Institutes for Health (NIH) campus, USA.

DNA Databank of Japan (DDBJ)
http://www.ddbj.nig.ac.jp

Genome Sequence DataBase (GSDB)
http://seqsim.ncgr.org/
The National Center for Genome Resources, Genome Sequence Database.
The server is a supercomputer with genomic algorithm accelleration.
Other Genomic Databases and Utilities
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These are often specialised databases.
The International Immunogenetics Database (IMGT)
http://imgt.cnusc.fr:8104
Contains expertly annotated sequences and alignment tables for Ig, TCR and MHC sequences.
Human Genome Map Database (HuGeMap)
http://www.infobiogen.fr/services/Hugemap
Genetic and physical maps of the human genome. Connected with the gene radiation hybrid mapping database RHdb.
UTR Home Page
http://bigarea.area.ba.cnr.it:8000/EmbIT/UTRHome/
Internet resources for sequence analysis of 5' and 3' untranslated regions of eukaryotic mRNAs. Includes specialised UTR databases and tools for analyses of UTR regions.
Sequence Search & Retrieval
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Integrated Database Retrieval Systems
Entrez
http://www.ncbi.nlm.nih.gov/Entrez/
Start here for pretty much anything!

Sequence Retrieval System (SRS)
http://www.seqnet.dl.ac.uk/srs/srsc

The Institute for Genomic Research (TIGR), Human Gene Index (HGI) Sequence Search
4-1-2-DDPDE/USA
http://www.tigr.org/tdb/hgi/searching/hgi_seq_search.html
Search for nucleotides and peptides.

TIGR HGI Reports
3-1-2-DDcW/USA
http://www.tigr.org/tdb/hgi/hgi_info.html
Retrieve sequences identified by EST ID, GenBank number etc.

TIGR HGI Gene Expression Data
4-2-1-DDcW/USA
http://www.tigr.org/tdb/hgi/searching/hgi_xpress_search.html
Search for tissue specific transcripts e.g. "lung". cDNA libraries can also be searched.

TIGR HGI Name Search
5-1-2-DDW/USA
http://www.tigr.org/tdb/hgi/searching/hgi_name_search.html
Search for a sequence by the name of a gene product e.g. insulin.

Genome Database (GDB)
http://hgmp.mrc.ac.uk/gdb or http://gdbwww.gdb.org/
Funding for this project has been withdrawn. This valuable database will remain online, but it should be noted that no new entries will be recorded after 31st July 1998.

GENATLAS (*)
5-5-2-DUWI/France
http://bisance.citi2.fr/GENATLAS/
A comprehensive, easy to use site. Search gene, marker or phenotype or linkage databases. Useful, relevant links provided in the results. The user can also locate the desired gene from a graphical clickable map of disease related or other mapped genes on a chromosome.

Gene Cards (*)
http://bioinfo.weizmann.ac.il/cards/
A very useful site providing comprehensive information and links. Direct links to GenBank, SWISS-PROT and MedLine. Includes synonyms, similar genes in other organisms, gene products and details about disorders.

Sequence Identification (BLAST, FASTA etc.)
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The Sanger Centre Database Search Services
5-2-5-DDPDFWE/UK -Clean, simple design.
http://www.sanger.ac.uk/DataSearch/
BLAST and WU-BLAST 2.0 searches which can be refined to finished and/or unfinished genomic sequences.

BLAST 2 Similarity Search (EMBNet)
5-3-2-PUWE/Switzerland
http://www.ch.embnet.org/software/frameBLAST.html
WU-BLAST 2.0 similarity searches.

BLAST2 Search with Post-processing (EMBL)
4-3-2-PUW/Germany
http://dove.embl-heidelberg.de/Blast2/
WU-BLAST 2.0 search with post-processing.

FASTA 3 (EMBL)
http://www2.ebi.ac.uk/fasta3/
FASTA 3 similarity search.

FASTA
http://www2.igh.cnrs.fr/bin/fasta-guess.cgi
FASTA similarity search and a clean, basic and simple interface.

Blitz
http://www.ebi.ac.uk/searches/blitz.html

Beauty
http://dot.imgen.bcm.tmc.edu:9331/seq-search/protein-search.html
Beauty is an enhanced BLAST search, returning output which predicts the function of the protein being tested.
Sequence Alignment
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Analysis and Annotation Tool for Finding Genes in Genomic Sequences
5-3-2-DcDPDFWE/USA
http://genome.cs.mtu.edu/aat.html
Identifies genes in a DNA sequence by comparing it to cDNA and protein sequence databases (including those at HGI, TIGR, dbEST, Swiss-Prot and nr).

Pairwise Sequence Alignment
3-4-2-DcUPUFWE/USA
http://genome.cs.mtu.edu/align/align.html
Computes the global alignment between two sequences. Compare DNA with DNA, cDNA or protein. For DNA and cDNA, settings (gap open penalty, gap extension etc.) can be defined.

Multiple Sequence Alignemnt with MAP
4-3-2-DcUPUFWE/USA
http://genome.cs.mtu.edu/map/map.html
Calculates the global alignment of DNA or protein sequences using an algorithm which computes the best overlapping alignment without penalising terminal gaps. Long internal gaps in short sequences are not penalised.

Network Protein Sequence Analysis
5-4-1-PUW/France
http://pbil.ibcp.fr/NPSA/npsa_clustalw.html
ClustalW multiple sequence alignment.

ALIGN
5-1-1-DUPUWE/France
http://www2.igh.cnrs.fr/bin/align-guess.cgi or http://genome.eerie.fr/fasta/align-query.html
Applies the BLOSUM50 matrix to deduce the optimal alignment between two sequences.

Multiple Sequence Alignment with Hierarchial Clustering
5-5-3-PUW/France
http://www.toulouse.inra.fr/multalin.html
Sequence alignment with a colour output where differing or similar amino acids in the alignment can be highlighted.

Colour INteractive Editor for Multiple Alignments (CINEMA)
http://www.biochem.ucl.ac.uk/bsm/dbbrowser/CINEMA2.1/
A comprehensive and popular site. Allows the user to visualise and manipulate aligned protein sequences.
Makes use of Java. I recommend you access this site from a fast workstation!

VSNS BioComputing Division Multiple Alignment Resource Page
http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/
An excellent, comprehensive resource for multiple sequence alignment, software and tutorials.

cDNA Databases
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TIGR Human cDNA Mapping Project
5-1-1-DcW/USA
http://www.tigr.org/tdb/hummap/hummap.html
Search by STS to retrieve individual STS reports, by GenBank, THC or HC number for transcripts with mapped STS's or by Chromosome number to see a list of all of the transcripts mapped to date, for example, on chromosome 16.

Via OMIM
You can search for a 'disease gene' at OMIM. Click the "DNA" button in the results display and follow the link to the mRNA sequence. Note the absence of U (uracil): this sequence is referred to in GenBank reports as mRNA, but the sequence is a cDNA sequence.
http://www.nih.gov
Mutation Databases
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Human Gene Mutation Database
4-2-2-DUW/UK
http://www.uwcm.ac.uk/search/mg/allgenes?
Enter a GDB accension number, disease name, gene name or symbol to retrieve well presented information about the different mutation types, information and links.

Protein Mutation Database
Check this site!
http://www.genome.ad.jp/htbin/bfind_pmd
COMMENTS

MITOMAP
Check this site!
http://infinity.gen.emory.edu/mitomap.html
Mitochondrial DNA database.

Breast Cancer Mutation Database
Check this site!
http://www.nchgr.nih.gov/Intramural-research/lab_transfer/bic/
COMMENTS
New Sequence Submission
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EMBL
http://www.ebi.ac.uk/subs/emblsubs.html

BankIt (GenBank)
http://ncbi.nlm.nih.gov/
Open Reading Frame (ORF) Finder
[Top]
ORF Finder
http://www.ncbi.nlm.nih.gov/gorf/gorf.html
Finds likely open reading frames in a sequence.
Sequence Translation
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Nucleotide to Protein (Expasy)
5-2-1-DUW/Switzerland
http://www.expasy.ch/www/dna.html
Translates a nucleotide sequence (DNA/RNA) into a protein sequence (amino acids).

Nucleotide to Protein (EMBL)
5-4-1-DUW/UK
http://www.ebi.ac.uk/contrib/tommaso/translate.html
Translates a nucleotide sequence into a protein sequence.

Forward and Reverse Translation
5-5-2-DUPUFWE/UK
http://www.sanger.ac.uk/Software/Wise2/genewiseform.shtml
Translate a protein sequence into a genomic DNA sequence, and vice versa.
This is a WWW interface to the pgwise software application. Those who are proficient with this package may like to take advantage of it's extra capabilities by adding execution critera.

Protein and cDNA Translation
5-4-2-DcUPU/UK
http://www.sanger.ac.uk/Software/Wise2/protein2cdna.shtml
Translate a protein sequence into a cDNA sequence, and vice versa.
Protein Sequence Databases
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Translated EMBL (TrEMBL)
http://www.ebi.ac.uk/pub/databases/trembl
Database of all the protein coding regions stored in the EMBL database. Comprehensive, but (generally) at the cost of poor annotation.

SWISS-PROT
http://expasy.hcuge.ch/sprot/sprot-top.html
A database of protein sequences, translated from the EMBL genomic database. Protein sequences have been checked and annotated.

PIR
http://www_nbrf.georgetown.edu/pir/
Four databases: PIR1 is the most comprehensive with entries classified and annotated. PIR4 is the least comprehensive, with unencoded or untranslated entries.
Motif Databases
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Pratt Search (EMBL)
4-4-2-PU
http://www2.ebi.ac.uk/pratt/
Interactively identifies conserved patterns from a series of user-entered unaligned protein sequences.

PROSITE (via EBI)
http://www2.ebi.ac.uk/ppsearch/
Pattern search to identify conserved functional amino acid motifs. Scans a sequence against PROSITE (the primary motif database) with a graphical output.

PROSITE
http://expasy.hcuge.ch/sprot/prosite.html
The primary motif database. Take care! Motifs are often short, and a large number of false positives should be expected! Options are available to exclude those which most commonly lead to false results.

Protein Motif Fingerprints
http://www.biochem.ucl.ac.uk/bsm/dbbrowser/PRINTS.html
Protein 3D Structure Database
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Protein Databank
http://www2.ebi.ac.uk/pdb/index.shtml
Three dimensional protein structures which can be downloaded and viewed locally (viewer required) or viewed in a hypertext browser window (e.g. Netscape). The structures are experimentally determined by X-ray crystallography and nuclear magnetic resonance (NMR) imaging.
Protein Analysis Utilities
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Web Cutter - Restriction Enzyme Mapping Utility
http://www.medkem.gu.se/cutter/
Map restriction enzyme sites on your sequence. Easy to use and comprehensive options.

Protein Colourer
5-2-1-PUW/UK
http://www.ebi.ac.uk/htbin/visprot.pl
Colour a protein sequence (raw text or SWISS-PROT Acc. No.) by properties e.g. hydrophobicity.

Residue Periodicity
Review this site
http://o2.dbuoa.gr/FT/
Study the periodicity of residues in a protein sequence.

Compute the Theoretical pI and Mr
5-1-2-PUW/Switzerland
http://www.expasy.ch/ch2d/pi_tool.html
Calculates the theoretical pI or molecular mass of a protein, whose sequence is entered by the user, or referred to as a SWISS-PROT or TrEMBL entry.

Random Protein Sequence Generator
5-5-2-PUW/Switzerland
http://www.expasy.ch/sprot/randseq.html
Random protein sequence generator! Output in FASTA format (the format most commonly required by bioinformatics search sites).
PCR Primers & Probes
[Top]
Primer 3
5-5-2-DUW/Norway
http://www2.no.embnet.uio.org/primer/primer3.cgi?
Select PCR primers for your nucleotide sequence.

HGMP-RC Primers Database
http://www.hgmp.mrc.ac.uk/local-data/Primers.html

EBI Primers Database
http://www.ebi.ac.uk/primers_home.html

Molecular Probe Data Base (MPDB or MOLPROBE)
http://www.biotech.ist.unige.it/interlab/mpdb.html
Databases of Non-Human Sequences
[Top]
Berkeley Fly Database
5-5-2-DDW (UI)/USA
http://www.fruitfly.org/bfd/
Search for sequences by name or map location, and optionally view a clickable image of sequenced contigs aligned alongside the fly chromosomes. Searches can be limited to available sequences only. Retrieve P1, BAC or cosmid genomic clones, P element insertion lines, YAC, STS and more.

The Institute of Genomic Research Databases
http://www.tigr.org/tdb/tdb.html
Many databases including microbial, parasites, human, human cDNA, mouse, rat, Arabidopsis, zebrafish, and others.
Utilities for Non-Human Sequences
[Top]
European Drosophila Genome Project BLAST server
5-4-3-DDPDFWE/UK
http://edgp.ebi.ac.uk/www-blast.html
Search using the WU-BLAST 2.0 (gapped aligned) or the original BLAST (which does not allow gaps). The database includes Drosophila genomic data, EST's, STS's, P element sites, transposons, repeats, and proteins.

Berkeley Drosophila Genome Project BLAST Searches
5-4-3-DDFWE/USA
http://www.fruitfly.org/blast/
Search for your sequence using the WU-BLAST 2.0 algorithm for D. melanogaster sequence data, including EST's, genomic sequences, STS's or sequences derived from them, P element insertion sites and transposons. (责任编辑：泉水)

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