Friday, October 9, 2009

Biological Databases and Bio-informatics

Protein related databases

  • UniProt - the universal protein resource (including UniProtKB -Swiss-Prot and TrEMBL-, UniRef, UniParc)
  • Around UniProtKB - links to related databases and portals
    • HAMAP - Portal to microbial UniProtKB/Swiss-Prot entries
    • SwissVar - Portal to human diseases and variant information in UniProtKB/Swiss-Prot
    • UniPathway - Metabolic pathways database
    • ViralZone - Portal to viral UniProtKB/Swiss-Prot entries
    • HPI - Human Proteomics Initiative
    • PPAP - Plant Proteome Annotation Project
    • Tox-Prot - Toxin Annotation Project
  • NCBI protein resources
  • InterPro - Integrated Resources of Proteins Domains and Functional Sites
  • PROSITE - Database of protein families and domains
  • BLOCKS - BLOCKS db
  • Gene3D - Structural and Functional Annotation of Protein Families
  • Panther - Functional classification system
  • Pfam - Protein families db (HMM derived) [Mirrors at JFRC (USA), CCBB (South Korea) Institute, UK, Karolinska Institutet (Sweden)]
  • PIRSF - Protein classification system
  • PRINTS - Protein Motif fingerprint db
  • ProDom - Protein domain db (Automatically generated)
  • PROTOMAP - An automatic hierarchical classification of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL proteins
  • SBASE - SBASE domain db
  • SMART - Simple Modular Architecture Research Tool
  • SUPERFAMILY - Library of profile HMMs representing all proteins of known structure
  • STRING - Search Tool for the Retrieval of Interacting Genes/Proteins
  • TIGRFAMs - TIGR protein families db
  • BIND - Biomolecular Interaction Network Database
  • DIP - Database of Interacting Proteins
  • MINT - Molecular INTeraction database
  • HPRD - Human Protein Reference Database
  • IntAct
  • BioGRID - General Repository for Interaction Dataset
  • PPI - JCB Protein-Protein Interaction Website
  • PMD - Protein Mutant db


Protein 3D structure related databases

  • PDB - Protein Data Bank
  • PDBTM - Protein Data Bank of Transmembrane Proteins
  • BioMagResBank - Repository for data on proteins, peptides, and nucleic acids from NMR spectroscopy
  • SWISS-MODEL Repository - Automatically generated protein models db
  • ModBase - Db of comparative protein structure models
  • CATH - UCL BSM structural classification of proteins
  • SCOP - Structural classification of proteins [ Mirrors]
  • HCA - Hydrophobic Cluster Database
  • Molecules To Go - Molecules To Go (formerly known as Molecules R Us), browser for PDB
  • BMM Domain Fishing - Biomolecular Modelling Laboratory (ICRF) protein domain fishing
  • Relibase - Receptor/ligand complexes db [Mirror in USA]
  • CCDC - Cambridge Crystallographic Data Center (Cambridge Stuctural Db (CSD))
  • HSSP - Homology-derived secondary structure of proteins db
  • MutaProt - Comparison of PDB files which differ by point mutations
  • DisProt - Database of Protein Disorder
  • SWISS-3DIMAGE - 3D images of proteins and other biological macromolecules
  • BioImage - Biological image db (contains imaging data on macromolecules)


Proteomics databases and links

Gel-based data


Mass spectrometry data

  • GPMdb - Global Proteome Machine Database
  • OPD - Open Proteomics Database
  • PeptideAtlas - peptides identified in tandem mass spectrometry proteomics experiments
  • PRIDE - PRoteomics IDEntifications database
  • Tranche - Peer-to-peer distributed file system


Nucleotide and related databases

  • EMBL - EMBL Nucleotide sequence db (EBI)
  • Genbank - GenBank Nucleotide Sequence db (NCBI)
  • DDBJ - DNA Data Bank of Japan
  • dbEST - dbEST (Expressed Sequence Tags) db (NCBI)
  • dbSTS - dbSTS (Sequence Tagged Sites) db (NCBI)
  • Ensembl - Genome database for vertebrates and other eukaryotic species
  • UCSC Genome Browser
  • AsDb - Aberrant Splicing db
  • ACUTS - Ancient conserved untranslated DNA sequences db
  • Codon Usage Db
  • EPD SIB- Eukaryotic Promoter db
  • HOVERGEN - Homologous Vertebrate Genes db
  • IMGT - ImMunoGeneTics db [Mirror at EBI]
  • RDP - Ribosomal db Project
  • PLACE - Plant cis-acting regulatory DNA elements db
  • PlantCARE - Plant cis-acting regulatory DNA elements db
  • smiRNAdb SIB- Information about mammalian small RNAs
  • ssu rRNA - Small ribosomal subunit at the European ribosomal RNA database
  • lsu rRNA - Large ribosomal subunit at the European ribosomal RNA database
  • 5S rRNA - 5S ribosomal RNA db
  • greengenes - 16S rRNA gene database and workbench
  • tmRNA Website
  • tmRDB - tmRNA dB
  • tRNA - tRNA compilation from the University of Bayreuth
  • RNA editing - RNA editing site
  • RNAmod db - RNA modification db
  • MPDB - Molecular probe db
  • VectorDB - Vector sequence db


Carbohydrates resources


Species specific databases

Human

Vertebrates


Mitochondrion and chloroplast

  • GOBASE - Organelle Genome Database
  • MitoDat - Mendelian Inheritance and the Mitochondrion db (mitochondrial nuclear gen
  • C.caldarium - Cyanidium caldarium strain RK1 chloroplast genome


Insects


Invertebrates


Plants


Fungi


Bacteria


Archaea


Viruses and phages


Human mutation databases/resources

· HGMD - Human Gene Mutation db

· SVD - EBI Sequence variation db

· HGVbase

· HGVS - The Human Genome Variation Society

· GeneDis - Human genetic disease db

· The International HapMap Project

· dbSNP - Human single nucleotide polymorphism (SNP) db

· ALFRED - Allele Frequency Db

· SeattleSNPs - UW-FHCRC Variation Discovery Resource

· PicSNP - Catalog of non-synonymous SNP

· List of mutation databases from OMIM

· List of mutation databases from IMT (Finland)

· ADAbase - Human adenosine deaminase (ADA) mutation db

· Albinism Database

· Albumin Web site

· AR mutations - Human androgen receptor mutation db

· Antithrombin mutation db

· Asthma and Allergy gene db

· BIOMDB - Db of mutations causing tetrahydrobiopterin deficiencies

· BLMbase - Human BLM mutation db (Bloom syndrome)

· BTKbase - Human BTK mutation db (X-linked agammaglobulinemia)

· CC_dbMD The Congenital Cataract Mutation Database

· CD3Ebase - Human CD3E mutation db

· CD3Gbase - Human CD3G mutation db

· CD40Lbase - Human CD40 ligand mutation db

· CD40Lbase - Human CD40 ligand mutation db

· COL1/3 mutation - Human Type I and III collagen mutation db

· Connexin-deafness - Human connexins mutation db

· CFTR mutation - Human cystic fibrosis mutation db (CFTR)

· KMbloodDB - Blood disease genes db

· KMbrainDB - Brain disease genes db

· KMcancerDB - Cancer disease genes db

· KMearDB - Ear disease genes db

· KMeyeDB - Eye disease genes db

· KMheartDB - Heart disease genes db

· KMmuscleDB - Muscle disease genes db

· KMsyndromeDB

· MaiDB (autoimmune)

· G6PD - Human G6PD deficiency resource

· G6PDdb - Human G6PD mutation db

· GNAS1 - Human GNAS1 mutation db

· HAMSTeRS - The Haemophilia A Mutation db and Factor VII Resource site

· Haemophilia B mutation db- Factor IX

· HbVar - Hemoglobin variants db

· Hereditary hearing loss homepage

· LDLR mutation - Human LDLR mutation db (Familial hypercholesterolemia)

· LHR - Human luteinizing hormone (LH) receptor mutation db

· NCF1base - Human NCF1 mutation db

· NCF2base - Human NCF2 mutation db

· Neuromuscular diseases web site

· NCL - Neuronal Ceroid Lipofuscinoses mutation db

· OCRL1 - OCRL1 mutation db (Lowe Syndrome)

· OTCase - Human ornithine transcarbamylase (OTCase) website

· Cytochrome P450 alleles nomenclature

· IARC TP53 mutation db - International Agency for Research on Cancer

· Germline p53 mutation db - University of Prague db of germline p53 mutations

· PAHdb - Human phenylalanine hydroxylase (PAH) mutation db

· PAX2 mutation - Human PAX2 mutation db

· PAX6 mutation - Human PAX6 mutation db

· Prion - Wikipedia Prion and prion disease

· RAG1base - Human RAG1 mutation db

· RAG2base - Human RAG2 mutation db

· RB1base - Human retinoblastoma-associated protein (RB) mutation db

· RetNet - Retinal Information Network

· Retina International Scientific Newsletter - Information on Retinal genes, proteins and diseases

· Alsod.org - ALS/SOD1 genetic mutations db

· TSC2 - Cardiff-Rotterdam Tuberous Sclerosis (TS) db (Tuberin; TSC2)

· TGDB - Tumor gene db

· VMD2 mutation - Human VMD2 mutation db

· vWF mutation - Human von Willebrand factor (vWF) mutation db

· WRN - Human WRN mutation db (Warner disease)

· X-ALD mutation - Human ABCD1 mutation db


Gene(s)/protein(s) specific databases/resources


Post-translational modifications databases and resources

  • DSDBASE - Disulfide database (derived from 3D data)
  • GlycoSuiteDB - Db of glycan structures
  • LIPID MAPS - LIPID Metabolites And Pathways Strategy
  • GlycateBase - Database of glycation data for epsilon amino groups of lysines
  • O-GlycBase - O-glycosylated proteins db
  • Phospho.ELM - Phosphorylation sites db
  • Phosphorylation site db - Bacterial and archaeal phosphorylation sites resource
  • PhosphoSite - Db of phosphorylation sites in human and mouse proteomes
  • DOLOP Db of bacterial lipoproteins
  • UbiProt - Db of ubiquitylated proteins
  • RESID - Db of Amino Acid Modifications
  • Delta Mass - Db of mass of Post-Translational Modifications


Phylogenetics and taxonomy databases & resources

  • COG and KOG - Phylogenetic classification of proteins encoded in complete genomes
  • eggNog - Automated construction and annotation of orthologous groups of genes
  • EGO - Eukaryotic Gene Orthologs
  • Ensembl Compara - Genome-wide species comparisons
  • HOGENOM - Homologous Sequences in Complete Genomes Database
  • HOVERGEN - Homologous Vetebrate Genes Database
  • InParanoid - Eukaryotic ortholog groups
  • KO - KEGG Orthology:
  • Metazome - Phylogenomic analysis of metazoan gene families
  • Optic - Orthologous and paralogous transcripts in clades
  • OMA - Orthologs Matrix Project (OMA)
  • OrthoDB Hierarchical catalog of eukaryotic orthologs
  • OrthoMCL DB Ortholog grouping for protein sequences from multiple genomes
  • PhylomeDB - Database for phylomes (collections of phylogenetic trees for all proteins encoded in a given genome)
  • P-POD - Princeton Protein Orthology Database with an emphasis on providing information about disease-related genes
  • Protein Clusters - NCBI collection of related protein sequences (clusters)
  • PhyloFacts - Pre-calculated structural and phylogenomic analyses of protein families and domains
  • TreeFam - Tree families database of phylogenetic trees of animal genes
  • CluSTr - Automatic classification of UniProtKB proteins into groups of related proteins
  • HomoloGene - Automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes
  • ProtoNet - Classification of the proteins into hierarchical clusters
  • NCBI Taxonomy Browser
  • NEWT - UniProt Taxonomy Browser
  • The Tree of life - Collection of WWW pages on phylogeny and biodiversity of organisms
  • TreeBASE - Relational db of phylogenetic information


Gene expression databases and resources

  • 4DXpress - a database for cross-species expression pattern comparisons
  • ArrayExpress - MicroArray informatics at the EBI
  • Bgee SIB- Retrieve and compare gene expression patterns across species
  • BioGPS - The Gene Portal Hub
  • CleanEx SIB- database of gene expression profiles
  • ExpressDB - Yeast and E.coli RNA expression db
  • GeneX - An open source Gene Expression database
  • GEO - Gene Expression Omnibus
  • GXD - MGI Gene Expression Database (mouse)
  • RAD - RNA abundance db
  • SMD - Stanford microarray db
  • MILANO - Microarray Literature-based Annotation
  • Genevestigator - a multi-organism, novel type of online meta-analysis tool for gene expression
  • GEMLeR - Gene Expression Machine Learning Repository


Patents databases


References (bibliographic databases)


Dictionaries, protocols, courses, nomenclature, etc.


Biological software and databases catalog servers


Gateways (portals) to Life Science resources


Biological journals and publishers

Resources linking to journals home pages


Publishers

· Allen Press, Inc.

· ACS - American Chemistry Society publications

· AP - Academic Press has joined the Elsevier Group

· Alaken - Alaken, Inc.

· ASM - American Society of Microbiology publications

· Annual Reviews

· Arnold Publishers

· BioMed Central - The Open Access Publisher

· Bio-IT World - Technology for the Life Sciences

· BioScientifica Ltd

· Birkhauser Verlag Basel

· Blackwell Publishing - has joined the Wiley Group

· BMJ Group - British Medical Journal publishing group

· Cell Press

· Churchill Livingstone - has joined the Elsevier Group

· COB - The Company of Biologists Ltd

· CRC Press Online

· CSHL Press - Cold Spring Harbor Laboratory Press

· CSIRO - CSIRO Publishing

· CUP - Cambridge University Press

· CJP - Carden Jennings Publishing Co. Ltd

· Elsevier Science & Technology publishing

· FASEB publications

· G+B - Gordon and Breach Publishing Group has joined the Taylor & Francis Group

· HighWire Press

· Horizon Scientific Press

· Humana Press, Inc. - has joined the Springer family

· Informaworld

· IOS Press

· IR - Inter-Research Science Publisher

· JAMA - The Journal of the American Medical Association publications

· JL - John Libbey Eurotext

· Karger AG

· Editrice Kurtis

· LW&W - Lippincott Williams and Wilkins

· Martin Dunitz Publishers - has joined Informa Healthcare

· Mary Ann Liebert, Inc

· Elsevier Masson

· Elsevier Mosby

· Blackwell Munksgaard

· IAPC NAUKA - NAUKA International Academic Publishing Company (Russia)

· NRC Research Press

· OUP - Oxford University Press

· Parthenon Publishing Group

· Pharmaceutical Press

· Portland Press

· Pulsus Group Inc.

· Rockfeller University Press

· Sage Science Press

· SGM - Society for General Microbiology publications

· SIR - SIR Publishing

· Slack, Inc.

· Springer

· T&F - Taylor & Francis Group

· Thieme

· University of Chicago Press

· Urban and Fischer Verlag - has joined the Elsevier Group

· VSP - VSP International Science Publishers

· VZN - Verlag der Zeitschrift fur Naturforschung

· W de G - Walter de Gruyter and Co.

· WBS - W.B. Saunders Co. has joined the Elsevier Group

· Wiley - John Wiley and Sons [Mirror in the U.K.]

· Wiley-VCH


Bioinformatics journals and newsletters


Genomic newsletters


Miscellaneous


Biotechnology trade journals


General science journals


Some biological societies and organizations

  • APS - American Peptide Society
  • ASCB - The American Society for Cell Biology
  • ASHG - American Society of Human Genetics
  • ATC-LGCC - American Type Culture Collection
  • Biochemical Society
  • BSA - Botanical Society of America
  • CSBMCB - Canadian Society of Biochemistry and Molecular and Cell Biology
  • EFBF - European Federation of Biophysics
  • EGF - European Genetics Foundation
  • EMBO - European Molecular Biology Organization
  • ESEB - European Society for Evolutionary Biology
  • ESHG - European Society of Human Genetics
  • FAOBMB - Federation of Asian and Oceanian Biochemists and Molecular Biologists
  • FASEB - Federation of American Societies for Experimental Biology
  • FEBS - Federation of European Biochemistry Societies
  • HUGO - HUman Genome Organization
  • HUPO - HUman Proteome Organization
  • IUBMB - International Union of Biochemistry and Molecular Biology
  • IUPAC - International Union of Pure and Applied Chemistry
  • MSA - Mycological Society of America
  • PPI - Plasma Proteome Institute
  • PRF - Protein Research Foundation
  • SDB - Society for Developmental Biology
  • SGM - Society for General Microbiology
  • SICB - Society for Integrative and Comparative Biology
  • DOI - Digital Object Identifier foundation
  • BioJava Project - International association of developers of Java tools for bioinformatics
  • Bioperl Project - International association of developers of Perl tools for bioinformatics
  • Biopython Project - International association of developers of Python tools for bioinformatics
  • ISCB - International Society for Computational Biology
  • OMG LSR - Object Management Group Life Science Research task force


Biocomputing servers homepages

Europe

  • EBI - European Bioinformatics Institute
  • EMBnet - European Molecular Biology Network
  • EMBL - EMBL Biocomputing unit
  • SIB SIB- Swiss Institute of Bioinformatics
  • EMBnet CH SIB- Switzerland EMBnet node
  • ISREC SIB- ISREC/SIB Computational Cancer Genomics group (Lausanne / Swizerland)
  • CBRG - Computational Biochemistry Research Group (Zurich / Switzerland)
  • ABIM - Atelier BioInformatique (Marseille / FR)
  • B3E - Bioinformatique/Biostatistique/Biomathematique/Epidemiologie (Paris / FR)
  • Genethon - Genethon (Evry / FR)
  • GeneStream - Institut de Génétique Humaine (Montpellier / FR)
  • GENOSCOPE - Centre National de Séquencage (Evry / FR)
  • GenoStar - Consortium for the development of a bioinformatic platform
  • IGS - Information Génétique et Structurale (Structural and Genetic Information Laboratory) (Marseille / FR)
  • IMPBIO - Informatique, Mathématiques, Physique en Biologie moléculaire
  • Pasteur - Institut Pasteur (Paris / FR)
  • PBIL - Pole Bio-informatique Lyonnais (Lyon / FR)
  • Sanger - Sanger Centre (Hinxton / U.K.)
  • BMM - Biomolecular Modelling laboratory at ICRF (London / U.K.)
  • BSM - Biomolecular Structure and Modelling group at UCL (London / U.K.)
  • Manchester - Manchester University Bioinformatics unit (U.K.)
  • RIO - Roslin Institute Online (U.K.)
  • HUSAR - Biocomputing Service at DKFZ
  • AG BIODV - Software Development for Molecular Biology at Helmholtz Zentrum (Germany)
  • FLI - Genome Analysis in Complex Diseases, Ageing and Model Organisms (Germany)
  • MDC:Bioinf - Department of Bionformatic of the Max Delbruck Center for Molecular Medicine (Germany)
  • MIPS - Munich Information Centre for Protein Sequences (Germany)
  • PZR - Bioinformatics at the Proteome Center Rostock (Germany)
  • VSNS BCD - Virtual School of Natural Sciences Biocomputing Division from the University of Bielefeld (Germany)
  • BEN - Belgium EMBnet node
  • CBS - Center for Biological Sequence Analysis (Technical University of Denmark)
  • CSC BioBox - CSC; Finland EMBnet node
  • ABC - Agricultural Biotechnology Center (Budapest / Hungary)
  • Telethon Italy
  • CMBI - Center for Molecular and Biomolecular Bioinformatics; Netherland EMBnet node
  • BIO - Biotechnology Centre of Oslo; Norway EMBnet node
  • IBB - Institute of Biochemistry and Biophysics (Warsaw); Poland EMBnet node
  • IGC - Bioinformatics and Computational Unit of the Instituto Gulbenkian de Ciencia; Portugal EMBnet Node
  • Belozersky Institute - GeneBee Molecular Biology server (Moscow); Russia EMBnet node
  • MGS - Molecular Biological Server (Novosibirsk / Russia)
  • CNB - Centro Nacional de Biotecnologia; Spain EMBnet node
  • BMC - BioMedical Centre at Uppsala; Sweden EMBnet node
  • KISAC - Karolinska Institute (KI) Sequence Analysis Computer
  • LCB - Linnaeus Centre for Bioinformatics
  • SBC - Stockholm Bioinformatics Center

USA and Canada

  • NCBI - National Center for Biotechnology Information
  • ABCC - Advanced Biomedical Computing Center at the NCI
  • ACGT - Advanced Center for Genome Technology at the University of Oklahoma
  • BCM HGC - Baylor College of Medicine Human Genome Center
  • BDGP - Berkeley Drosophila Genome Project
  • BioTech - Life Sciences Resources and Reference Tools
  • Biotechnology - National Agricultural Library - Biotechnology
  • BMERC - Biomolecular Engineering Research Center
  • BROAD Institute
  • CBIL - Computational Biology and Informatics Laboratory at the University of Pennsylvania
  • CCB - Washington University Center for Computational Biology
  • CUBIC - Columbia University Bioinformatics Center / RostLab
  • JCVI - J. Craig Venter Institute
  • JGI - Doe Joint Genome Institute
  • NCGR - National Center for Genome Resources
  • NIH - Computational Molecular Biology at NIH
  • UCLA - UCLA Bioinformatics Institute
  • Bioinformatics & Research Computing at Whitehead Institute
  • CBR - Canadian Bioinformatics Resource (currently not working)
  • CCB - Centre for Computational Biology at the Hospital for sick children

Asia

  • APBioNet - Asia-Pacific Bioinformatics network
  • BIC-JNU - Bioinformatics Center of Jawaharlal Nehru University
  • BIDD - Bioinformatics & Drug Design group (National University / Singapore)
  • DIC - Bioinformatics Centre at the University of Pune
  • Japanese GenomeNet
  • NIG - National Institute of Genetics of Japan
  • KDRI - Kazusa DNA Research Institute
  • CBI - Peking Center of Bioinformatics; Chinese EMBnet node
  • MICRO-NET - Microbial Information Network of China
  • HKBIC - Hong Kong Bioinformatics Center
  • BRIC - Biological Research Information Center (Korea)
  • MGRC - Malaysian Genomics Resource Centre
  • BIC - BioInformatics Center of the National University of Singapore

Australia

  • APBioNet - Asia-Pacific Bioinformatics network
  • ANGIS - Australian National Genomic Information Service
  • ANU - Australian National University Genomic Interactions group
  • APAF - Australian Proteome Analysis Facility

Others

  • HUJI - Hebrew University of Jerusalem genomic and bioinformatics server
  • Weizmann Bioinfo/BCU - Weizmann Institute of Science Bioinformatics and Biological Computing
  • SANBI - South African BioInformatics Institute
  • BDT - Base de Datos Tropical (Sao Paulo / Brazil)
  • ICGEB - International Center for Genetic Engineering and Biotechnology (Trieste / Italy)


Biotechnology and pharmaceutical companies


Bio-informatics companies


Miscellaneous medical references sites


Miscellaneous scientific references sites


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