View source for Bioinformatics links

*[http://bioinformatics.ubc.ca/resources/links_directory/ Bioinformatics Links Directory]

==Databases==
*[[wikipedia:Biological_database]]
===General===
*[http://www.ebi.ac.uk/ European Bioinformatics Institute] &mdash; portal for research and services in bioinformatics, with databases of nucleic acid and protein sequences, and macromolecular structures - from the EMBL, Hinxton UK.
*[http://www.ncbi.nlm.nih.gov/ NCBI/GenBank (USA)] &mdash; offers many important databases (PubMed, GenBank, OMIM) and some tools.
*[http://www.ddbj.nig.ac.jp/ DDBJ (Japan)]

===Genomes===
*[http://www.tigr.org/tdb/mdb/mdbcomplete.html TIGR]
*[http://www.jgi.doe.gov/JGI_microbial/html/index.html JGI]
*[http://www.sanger.ac.uk/Projects/Microbes/ Sanger]
*[http://ncbi.nlm.nih.gov/Genomes/index.html NCBI]

===Lists of genomes in progress===
*[[Genome projects]]
*http://wit.integratedgenomics.com/GOLD/
*http://www.tigr.org/tdb/mdb/mdbinprogress.html
*[http://www.ensembl.org/info/data/download.html Ensembl genome download] (mainly Eukaryotes)
*[http://www.genomesonline.org/gold.cgi?want=Published+Complete+Genomes Complete Published Genome Projects: 524]

==Web servers==
*[http://molvis.sdsc.edu/visres/servers/titles.jsp World Index of BioMolecular Visualization Resources]
*[http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsitescan/ PDBSiteScan]
*[http://www.ebi.ac.uk/thornton-srv/databases/CSA/ Catalytic Site Atlas (CSA)] &mdash; a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure.
*[http://bioinfo3d.cs.tau.ac.il/SiteEngine/ SiteEngine] &mdash; Functional Sites Structural Search Engine; Recognizes regions on the surface of one protein that resemble a specific binding site of another.
*[http://sumo-pbil.ibcp.fr/cgi-bin/sumo-welcome SuMo]
*[http://astral.berkeley.edu/ ASTRAL] &mdash; The ASTRAL Compendium for Sequence and Structure Analysis.
*[http://www.molmovdb.org/ MolMovDB] &mdash; Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis.
*[http://scop.berkeley.edu/ SCOP: Structural Classification of Proteins]
*[http://ekhidna.biocenter.helsinki.fi/dali/start Dali Fold Classification] &mdash; based on exhaustive, all-against-all 3D structure comparison of protein structures in the Protein Data Bank
*[http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/ PDBsum] &mdash; provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank 
*[http://rna.tbi.univie.ac.at/cgi-bin/alifold.cgi Vienna RNA Secondary Structure Prediction]
*[http://blocks.fhcrc.org/ BLOCKS] &mdash; a service for biological sequence analysis
*[http://wikiomics.org/wiki/Searching_for_3D_functional_sites_in_a_protein_structure Searching for 3D functional sites in a protein structure]
*[[wikipedia:Structural genomics]]

==Data acquisition (search engines)==

===Keyword===
*[http://srs.ebi.ac.uk/ SRS] (tutorials can be found at http://www.icgeb.trieste.it/~netsrv/courses/RH/srs/ or http://www.no.embnet.org/Programs/DB/srs_tut.php3)
*[http://www.ncbi.nlm.nih.gov/Entrez/ Entrez] (tutorial can be fond at http://www.ncbi.nlm.nih.gov:80/Database/tut1.html)

===Similarity===
*[http://www.ncbi.nlm.nih.gov/BLAST/ BLAST]

==Multiple sequence alignment==
*[ftp://ftp.ebi.ac.uk/pub/software/ ClustalX (ftp)] (tutorial can be found at http://www.bioinf.org/molsys/ClustalX_tutorial.html)
*[http://www.mbio.ncsu.edu/BioEdit/bioedit.html BioEdit]
*[http://searchlauncher.bcm.tmc.edu/ BCM search launcher]
*[http://www.accelrys.com/products/gcg_wisconsin_package GCG]
*[http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html/ Lists]
*[http://www.charite.de/bioinf/strap/ STRAP] &mdash; Multiple Sequence Alignment

==Prediction==
*[http://alexander.compbio.ucsf.edu/~nomi/nnpredict.html NNPREDICT] &mdash; Protein Secondary Structure Prediction
*[http://automotif.bioinfo.pl/state.htm Pattern and profile searches Pattern and profile searches]

==Phylogenetic analysis==
*[http://paup.csit.fsu.edu/index.html PAUPp] (tutorial can be found at http://paup.csit.fsu.edu/Quick_start_v1.pdf)
*[http://www.megasoftware.net/ Mega2]
*[http://evolution.genetics.washington.edu/phylip.html PHYLIP]
*[http://taxonomy.zoology.gla.ac.uk/rod/treeview.html Treeview]
*[http://evolution.genetics.washington.edu/phylip/software.html List]

==Taxonomy==
*[http://www.sp2000.org/ Species 2000]
*[http://www.ubio.org/ uBio] &mdash; uses names and taxonomic intelligence to manage information about organisms
*[http://www.biolib.cz/en/main/ BioLib] &mdash; an international encyclopaedia of plants, fungi, and animals.
*[http://www.forestryimages.org/ Forestry Images]
*[http://www.iucnredlist.org/ The 2006 IUCN Red List of Threatened Species]

==Software==
*[http://www.biolinux.org/ BioLinux.org]
*[http://rutchem.rutgers.edu/%7Exiangjun/3DNA/ 3DNA]
*[http://skuld.bmsc.washington.edu/raster3d/raster3d.html Raster3D]
*[http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/ EMBOSS applications]

==Other==
*[http://www.bioinform.com/index.htm Bioinform] &mdash; bioinformatics news service.
*[http://www.bioinformatics.ca/ Bioinformatics.ca] &mdash; curated web directory of molecular biology and bioinformatics resources
*[http://www.bioinformatik.de/ Bioinformatik] &mdash; categorical web directory for bioinformatics theory - from the Univ. of Düsseldorf. Mathematics and Computer-based.
*[http://www.bioplanet.com/index.php Bioplanet Jobs] &mdash; bioinformatics jobs, education resources, bulletin board, CV posting.
*[http://cbr-rbc.nrc-cnrc.gc.ca/index_e.php Canadian Bioinformatics Resource] &mdash; dedicated to providing researchers with convenient, effective access to high-quality bioinformatics tools and databases.
*[http://restools.sdsc.edu/ CMS Molecular Biology Resources] &mdash; a compendium of tools for molecular biology, biotechnology, molecular evolution, biochemistry and biomolecular modeling.
*[http://cs.rockefeller.edu/index.php3?page=toolkit DNA and Protein Analysis Toolkit] &mdash; compendium of bioinformatics computing services from The Rockefeller University. Many different ways to analyse biomolecules.
*[http://megasun.bch.umontreal.ca/other/genomes.html Genome Programs] &mdash; links to online genomics resources - including the individual projects.
*[http://www.osaka-med.ac.jp/deps/bcc/mbs.html Molecular Biological Sites] &mdash; includes sequence search windows, as well as databases and tools related with proteomics and structural bioscience.
*[http://snowdeal.org/section/informatics/ Snowdeal.org] &mdash; a weblog that provides daily updates and links to news items and stories of interest to bioinformatics community.
*[http://bioinformatics.ubc.ca/resources/links_directory/ UBC Bioinformatics Centre Resource Directory] &mdash; currated and categorized database of links to the top bioinformatics and molecular biology resources on the web.
*[http://www.openscience.org/blog/ The OpenScience Project]
*[http://tanna.bch.ed.ac.uk/qg3.htm Quick guide to characteristics of metal sites in proteins]
*[http://www.ysbl.york.ac.uk/~alexei/sfcheck.html sfcheck] &mdash; a program for assessing the agreement between the atomic model and X-ray data or EM map.
*[http://www.omicsworld.com/ OmicsWorld]
*[http://www.liebertpub.com/publication.aspx?pub_id=43 OMICS: A Journal of Integrative Biology]
*[http://blaster.docking.org/zinc/ ZINC] &mdash; a free database of commercially-available compounds for virtual screening.
*[http://www.bio.sk/dir/ BIO.SK - Directory]

==Wikis related to Bioinformatics==
*[http://wikiomics.org/wiki/Main_Page Wikiomics.org] &mdash; ([http://wikiomics.org/wiki/User:Christoph User:Christoph])
*[http://omics.org/index.php/Main_Page Omics.org] &mdash; an openfree wiki site for -omes and -omics in Biotechnology and Bioscience. 
*[http://openwetware.org/wiki/Main_Page OpenWetWare.org]
*[http://rana.lbl.gov/drosophila/wiki/index.php/Main_Page AAA Wiki] &mdash; considers sequenced ''Drosophila'' genomes.
*[http://biodomain.org/index.php/Main_Page openfree BioDomain.org] &mdash; a list of biological domains.
*[http://www.biodirectory.com/biowiki/Main_Page BioDirectory.com]
*[[wikipedia:Bioinformatics]]
*[[wikibooks:Computational Biology]] (aka Bioinformatics)

[[Category:Bioinformatics| ]]