～推荐，生物学生应该知道的一些网站～

General bioinformatics gateways


http://www.ncbi.nlm.nih.gov/

National Center for Biotechnology Information homepage. A resource for public databases, bioinformatics tools and applications. Links to many useful sites and resources for bioinformatics software

http://www.ebi.ac.uk/

The EMBL European Bioinformatics Institute outstation. A resource for biological databases and software, much of which has excellent tutorial support

http://www.expasy.ch/

The ExPASy (Expert Protein Analysis System) Molecular Biology Server. Maintained by the Swiss Institute of Bioinformatics (SIB). Provides links, databases and software resources for the analysis of protein sequences, structures and expression

http://www.embl-heidelberg.de/

European Molecular Biology Laboratory homepage

http://www.gmd.de/Welcome.en.html

German National Center for Information Technology homepage. Has now merged with Fraunhofer-Gesellschaft (FhG); see updates on the FhG website

http://www.fraunhofer.de/english/

http://www.bioinformatics.leeds.ac.uk/

Bioinformatics Home Page maintained by the School of Biochemistry and Molecular Biology at Leeds University. Links to many bioinformatics resources

http://links.bmn.com/

The BioMedNet gateway to thousands of biological websites, includes a search facility and provides descriptions of each of the web sites listed

Genome projects



http://wit.integratedgenomics.com/GOLD/

Genomes OnLine Database, with links to genomic databases and progress reports on genome projects

http://www.genome.ad.jp/kegg/

Kyoto Encyclopedia of Genes and Genomes. A comprehensive Japanese site including metabolic maps

Computing notes

[ 本帖最后由 Tuexy 于 2009-3-11 19:08 编辑 ]

http://PlasmoDB.org/

PlasmoDB (Plasmodium falciparum

– malaria parasite)

http://mips.gsf.de/proj/thal/db/

MIPS Arabidopsis> thaliana Database (MAtDB)

http://www.arabidopsis.org/

The Arabidopsis Information Resource (TAIR)

http://flybase.bio.indiana.edu/

FlyBase (Drosophila melanogaster – the fruit fly)

http://www.acedb.org/

A C. elegans DataBase (AceDB). This URL directs to a database development site. For a useful  C. elegans resource try http://www.wormbase.org/

http://www.informatics.jax.org/

Mouse Genome Database (MGD)

http://www.ncbi.nlm.nih.gov/omim/

OnLine Mendelian Inheritance in Man (OMIM)

Genome and organism resources



http://www.ncbi.nlm.nih.gov/Genomes/index.html

NCBI Genomic Biology

http://wit.integratedgenomics.com/GOLD/

GOLD (Genomes OnLine Database)

http://www.nih.gov/science/models/

A useful selection of resources about model organisms used in biomedical research

http://www.tigr.org/tdb/mdb/mdbcomplete.html

TIGR Microbial Database. A listing of published microbial genomes and chromosomes and those in progress

http://genolist.pasteur.fr/

GenoList Genome Browser. Selected bacterial/fungal genomes

http://genome-[url]www.stanford.edu/Saccharomyces/[/url]
yeast_info.html

Yeast databases

http://www.ensembl.org/

Ensembl genome database project. A joint project between EMBL–EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on eukaryotic genomes

http://mips.gsf.de/

MIPS (Munich Information Center for Protein Sequences)

Database tools for viewing and annotating genome data

http://www.sanger.ac.uk/Software/Artemis/

Artemis. A DNA sequence viewer and annotation tool

http://www.acedb.org/Tutorial/brief-tutorial.shtml

A quick guide to AceDB (a C. elegans DataBase)

http://www.ensembl.org/apollo/

Apollo Genome Browser

http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map_search

Entrez Genome, the NCBI Map Viewer

http://genome.ucsc.edu/

The UCSC Genomes Bioinformatics Site, containing working drafts for the human genome and the mouse genome

Miscellaneous databases



http://www.nar.oupjournals.org./

Nucleic Acids Research homepage. Click on ‘Database Issue’ to see details of new or updated databases in the current year

http://biobases.ibch.poznan.pl/

http://rrna.uia.ac.be/ssu/

Non-coding RNA sequence databases

[ 本帖最后由 Tuexy 于 2009-3-13 19:36 编辑 ]

http://foldoc.doc.ic.ac.uk/foldoc/index.html

FOLD (Free On-Line Dictionary of Computing). A good place to look up meanings of computer jargon

SECTION B

http://www-structure.llnl.gov/Xray/101index.html

Excellent collection of notes on the principles of X-ray crystallography

SECTION C

Sequence databases



http://www.ebi.ac.uk/embl/

EMBL Nucleotide Sequence Database

http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html

NCBI GenBank

http://www.ddbj.nig.ac.jp/

DNA Data Bank of Japan

http://www.ebi.ac.uk/embl/Submission/

Webin. A sequence deposit tool for the EMBL Nucleotide Sequence Database

http://www.ncbi.nlm.nih.gov/BankIt/

BankIt. A WWW-based sequence deposit tool for NCBI GenBank

http://www.ncbi.nlm.nih.gov/Sequin/index.html

Sequin. An FTP-based sequence deposit tool for NCBI GenBank

http://us.expasy.org/sprot/

SWISS-PROT and TrEMBL. Protein databases

Organism databases



http://bmb.med.miami.edu/EcoGene/EcoWeb/

EcoGene (E. coli)

http://www.ecocyc.org/

EcoCyc. Encyclopedia of E. coli genes and metabolism

http://genolist.pasteur.fr/Colibri/

Colibri (E. coli)

http://genolist.pasteur.fr/SubtiList/

SubtiList (B. subtilis)

http://genome-[url]www.stanford.edu/Saccharomyces/[/url]

Saccharomyces Genome Database (SGD)

http://www.neb.com/neb/inteins.html

InBase, the New England Biolabs Intein Database

http://www.ncbi.nlm.nih.gov/UniGene/

UniGene, a division of GenBank automatically partitioning GenBank sequences (including genomic fragments, ESTS etc) into a non-redundant set of gene-oriented clusters

http://www.pdb.org/ and

http://www.rcsb.org/pdb/

The worldwide repository for the processing and distribution of 3D biological macromolecular structure data

http://pir.georgetown.edu/

Protein information resource database of annotated protein sequences

SECTION D

http://www.ncbi.nlm.nih.gov/Entrez/

NCBI Entrez

http://www.genome.ad.jp/dbget/

GenomeNet Japan DBGET/Link

http://srs6.ebi.ac.uk/

WWW-based SRS (sequence retrieval system) at EBI

http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz
?-page+databanks+-newId

SRS available databases

SECTION E

Sequence similarity using dot plots


http://www.cgr.ki.se/cgr/groups/sonnhammer/Dotter.html

Dotter program from the Karolinska Institutet\'s Centre for Genomics Research

Sequence similarity searches


http://www.ebi.ac.uk/fasta33/index.html

FASTA searches at EBI

http://www.ncbi.nlm.nih.gov/BLAST

BLAST and PSI-BLAST searches at NCBI

http://www.ncbi.nlm.nih.gov/BLAST/filtered.html

Notes on low complexity filtering with BLAST

SECTION F

Multiple sequence alignment

[ 本帖最后由 Tuexy 于 2009-4-16 13:57 编辑 ]

http://www.ebi.ac.uk/clustalw/

ClustalW online at EBI

ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/

ClustalW and ClustalX software

Protein family databases


http://ca.expasy.org/prosite/

PROSITE database

http://bioinf.man.ac.uk/dbbrowser/PRINTS/

PRINTS database

http://www.blocks.fhcrc.org/

BLOCKS   database

http://www.sanger.ac.uk/Software/Pfam/

Pfam protein domain family database

http://smart.embl-heidelberg.de/

SMART protein domain family database

http://prodes.toulouse.inra.fr/prodom/2002.1/html/home.php

Prodom protein domain style=\"mso-spacerun: yes\">  family database

http://www.ebi.ac.uk/interpro/

InterPro, integrated protein family databases, at EBI

谢楼主有心了,这么多