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bioinfo2

Functional genomics

Transcriptomics databases

Microarray Bioinformatics at EBI
Arrayexpress at the EBI
Expression Profiler at EBI
Documentation for Expression Profiler
Gene Expression Atlas - Large Scale Meta-Analysis of Public Microarray Data
GEO Gene Expression Omnibus at NCBI
NCBI Sequence Read Archive
MaRe Microarray Retriever
Stanford Microarray Database
Yale Microarray Database
JCV Institute Genomics
NIH ENCODE Project: ENCyclopedia Of DNA Elements
NGFN German National Functional Genomics Network
Genevestigator
GeneCAT - Gene Co-expression Analysis Toolbox
CATMA - A complete Arabidopsis Transcriptome MicroArray
The Arabidopsis Information Resource - TAIR
AFGN Arabidopsis Functional Genomics Network
Microarray Gene Expression Data Society
Stanford Functional Genomics Facility

Transcriptomics tools

NIH - Guide to Microarray Data analysis
Microarray Tools at NCI
HSLS: Microarray, SAGE and other gene expression data analysis tools
J-Express microarray analysis free version
MicroArray Explorer tool for Data Mining Gene Expression Patterns
Tools from the Eisen Lab
BioConductor Project - Open Source Software for Bioinformatics
R and Bioconductor Manual (Thomas Girke)
Babelomics - Systems biology microarray data mining
TIGR Microarray Software
RNA-Seq software ERANGE
Broad Institute Genecluster 2.0
dChip Software: Gene Expression Microarray and SNP Microarray Analysis
NASC Affymetrix Service: Analysis hints
Analysis of Affymetrix data using Excel
Affymetrix - NetAffx TM Analysis Center
MapMan - integrative view of microarray data and metabolic maps
GenMAPP Gene Map Annotator and Pathway Profiler

Proteomics databases and search engines

ExPASy Swiss 2Dpage
WORLD-2DPAGE Index to 2D-PAGE databases and services
ExPASy Peptide Mass Tool
ExPASy Mass Search
ExPASy MultIdent Peptide Mass Fingerprinting Tool
MASCOT Peptide Mass Fingerprint
SEQUEST MS proteomics search engine
Phenyx MS protein search engine (GeneBio/SIB)
X! Tandem MS search engine
OMSSA ms/ms search engine
UCSF Mass Spectrometry Facility Protein Prospector
PROWL protein and MS tools
PRIDE - Proteomics Identifications Database
PeptideAtlas
GPMDB proteomics database
Human Protein Atlas
Tranche - Secure P2P for Scientific Data Dissemination
ISPIDER MS meta protein database search
Protein Identifier Cross-Reference Service
NIH Histone Sequence Database
Phospho.ELM Database of phosphorylation sites
PhosphoPep Phosphopeptide systems biology database
Human Protein Reference Database

Proteomics post translational modifications

ExPASy - FindMod tool
ExPASy - QuickMod - MS/MS modified peptide search tool
RESID Database of protein modifications
Delta Mass PTM database (ABFR)
Unimod database - protein modifications for MS
Unimod - Modification naming guidelines
PRIDE Modification Search
PRIDE modification ontology lookup service (OLS)
ExPASy - Sulfinator tool Tyr sulfination sites predictor
NetPhos 2.0 Server STY phosphorylation site predictor
HUPO PSI Protein Modification Documentation

Proteomics software

TPP Trans-Proteomic Pipeline
SASHIMI MS proteomics pipeline
OpenMS / TOPP open source MS proteomics pipeline
MaxQuant
ICPLQuant
Scaffold protein identification framework (by Proteome Software)
mMass - Open Source Mass Spectrometry Tool
PeptideProphet MS proteomics prediction tool
ProteinProphet MS proteomics prediction tool
MassTRIX Metabolomics mass to pathway mapper

Proteomics organisations and standards

HUPO - Human Proteome Organisation
UniProt Chordata protein annotation program
HUPO Proteomics Standards Initiative
MASC Arabidopsis Proteomics Standards Subcommittee
mzML Specification | HUPO Proteomics Standards Initiative
Mass spectrometry data formats - Wikipedia
gabi Arabidopsis Proteomics Data
Proteomics from Angelika Görg
Boston University Biology Proteomics Resource
Deutsche Gesellschaft für Proteomforschung
Swiss Proteomics Society
SWISS Proteomics Society Proteomics Links
Proteome commons
ISB NHLBI Seattle Proteome Center
IonSource Proteomics Resource Links

Protein-Protein Interactions

EBI IntAct Project
DIP - Database of Interacting Proteins
DIP DLRP Database of Interactiong Proteins
BOND - Biomolecular Object Network Database
BioGRID - General Repository for Interaction Datasets
MINT - Molecular Interactions database
GNP Genome Network Platform
MIPS MPact Protein Interaction and Complex DB
MIPS Mammalian Protein-Protein Interaction Databank
The JCB Protein-Protein Interaction Website
GeneInfinity's Protein Interaction Analysis page
HPRD Human Protein Reference Database
Human Protein Interaction Database
NCBI HIV Human protein interaction database
UniHI MDC Unified Human Interactome
MIPS Yeast Protein-Protein-Interaction and Complex Viewer
Yeast Protein complex database
HomoMINT predicted human interaction network
PIPs Human Protein Interaction Prediction Database
Domino Domain peptide interaction database
VirusMINT
OPHID Interologous interaction database
PathBlast - Comparison of interaction networks between organisms
iHOP - Information Hyperlinked over Proteins
String: functional protein association networks
3DID - 3D interacting domains
DOMINE Database of Protein Domain Interactions
PSI-MI HUPO Standard for interactions
BioPAX - data exchange for biologicaql pathway data
Graphviz - Open Source Graph Visualization Software
Cytoscape - open source software for interaction visualization and integration
Osprey - protein interaction viewer
Osprey - protein interaction molecular modeling
visANT - Visual Analysis Tool for Biological Networks and Pathways
aiSee - commercial Graph layout software
NAViGaTOR - Network Analysis, Visualization, & Graphing TORonto

miRNA

RNA Molecular Biology Tuschl Lab
miRBASE microRNA database Sanger Institute
Rfam RNA families database of alignments and CMs Sanger Institute
The siRNA user guide - Tuschl Lab
microRNA.org: A resource for predicted microRNA targets and expression
OligoWalk Web Server for siRNA design
AsiDesigner siRNA design pipeline

Systems Biology

System Biology Information Resources

BioModels.NET
The Reactome Project
Panther Classification Systems - Panther Pathways
Human Metabolome Database
KDBI - Kinetic Data of Biomolecular Interactions
SBML Systems Biology Markup Language
SBGN Systems Biology Graphical Notation Standardization
The International Society for Systems Biology
Systems Biology Portal www.systems-biology.org
The Systems Biology Institute - Tokyo
US National Centers for System Biology
Systems Biology at UC San Diego
Systems Biology in Germany
HepatoSys - Network Systems Biology
SystemsX - The Swiss Initiative in Systems Biology
YSBN The Yeast Systems Biology Network
Nature web focus: Systems biology: a user's guide
Systems Biology Wikipedia

Systems Biology Modeling Tools

Systems Biology WorkBench SBW package
JDesigner: A Biochemical Network Layout Tool
Jarnac biochemical simulation package
Pasadena Twain ODE solver of the SWB package
CADLIVE - network construction system
Dizzy stochastic simulations tool
CellDesigner - a modeling tool for biochemical networks
SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks
Cellware - Modeling and Simulation Tool
E-Cell project
COPASI - Complex Pathway Simulator
Gepasi - Biochemical Kinetics Simulator
Dynetica - a simulator of dynamic networks
JSim - a Java based simulation system
STOCKS - Stochastic kinetic simulations
Basis Gillespie Stochastic Simulator
CaliBayes - Bayesian calibration of biological simulators
JWS Online - Online Cellular Systems Modelling
PyBioS - web server for modeling and simulation of cellular systems
Virtual Cell Internet simulation server at NRCAM

Small molecules

Human Metabolome Database
KEGG Drug Database
KEGG Ligand Database
ChEBI - Chemical Entities of Biological Interest
MSD Ligand Chemistry in PDB
NCBI PubChem Compound
NCBI PubChem Substance
NLM SIS Chemical Information
NCI-3D Search
ChemIDplus
CHEMINFO: Chemical Information Sources from Indiana University
FAF-Drugs: Free ADME/tox Filtering
OpenBabel format conversion tool for drugs
Java Molecular Editor at RPBS
JME Molecular Editor by Peter Ertl
SuperPred Drug Target Prediction Server

Annotation

Gene Function Resources

Gene Ontology (GO) Consortium
QuickGO - GO Browser at EBI
AmiGO - GO Browser
Ontology Lookup Service (OLS)
GOA - Gene Ontology Annotation Project at EBI
GOStat - find statistically overrepresented GO terms
Gene Ontology Tools for Gene Expression Analysis
Sequence Ontology Project
Online Mendelian Inheritance in Man
GeneCards Weizmann
Genetic Association Database

Integrated annotation services

NIH - DAVID Annotation tools
eFamily Project - Grid integrating of protein database annotations
DAS - Distributed Annotation System
DAS registry server at Sanger - available DAS servers
SPICE - DAS Client
EnsEMBL Genome Browser DAS client
Dasty - DAS client

Gene prediction services

Glimmer Microbial Gene-Finding System
NCBI Glimmer3
GrailExp Grail Experimental Gene Discovery Suite
BCM Gene Feature Searches
CBS HMMgene server
CBS NetGene2 server
CBS NetPlantGene server
CBS Genome Atlas
GeneMark
WebGeneMark
Eukaryotic WebGeneMark
GENSCAN (C. Burge)
SplicePredictor
ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences
EBI Wise2 matches protein to genomic DNA
Lowe Lab tRNAscan-SE Search Server

Promotor prediction services

CBS NetStart 1.0 server Translation Start
CBS Promoter 2.0 server
WWW Promotor Scan Pol II
EPD Eukaryotic promotor database
TFM Explorer
TFM-Scan
TFSEARCH - Transcription Factor Search
TRANSFAC database at Biobase Biological Databases
ORegAnno: Open Regulatory Annotation
JASPAR Transcription factor database
JASPAR Transcription factor database paper
MotifMogul - Multiple Transcription Factor Binding Sites Algorithms
Regulatory Sequence Analysis Tools (RSAT)
DIALIGN - multiple sequence alignments to find conserved regulatory elements
The Gibbs Motif Sampler
MEME MAST motif discovery and search
DiRE identification of DIstant Regulatory Elements of co-regulated genes
ConTra - identification of conserved transcription factor binding sites

Databases

Pathways

KEGG: Kyoto Encyclopedia of Genes and Genomes
ExPASy - Biochemical Pathways
NCI BioCarta - Pathways
PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System
Signaling Gateway - Cell Signaling Resource Nature
Reactome Project
BioCyc Database Collection
MetaCyc Encyclopedia of Metabolic Pathways
NCI Nature Pathway Interaction Database
IUPHAR receptor database
LGICD Ligand-gated ion-channel database
AraCyc - Pathway Database of Arabidopsis thaliana
Invitrogen Pathways
NetPath human signal transduction pathways
BBID-Biological Biochemical Image Database
Signal Transduction - Biochemweb.org virtual library
BioPAX - data exchange for biological pathway data
visANT - Visual Analysis Tool for Biological Networks and Pathways
MapMan - integrative view of microarray data and metabolic maps
GenMAPP Gene Map Annotator and Pathway Profiler
Biological Networks
Comparative Pathway Analyzer
PaLS Pathway and Literature Strainer (gene set annotation tool)
ProdoNet Prokaryotic gene list pathway annotator
GraphWeb: analysis of biological networks
Network Analysis Tools (NeAT)

Enzymes

Enzyme Database - BRENDA
IntEnz EBI Enzyme Database
Catalytic Site Atlas - CSA (EBI)
REBASE The Restriction Enzyme Database
Protein Kinase Resource
Kinase.com Global kinome analysis
NetworKIN kinase substrate relationship prediction

Motifs Profiles Domains

Interpro Domain and Profile Database
ExPASy - PROSITE
ExPASy - ScanProsite tool
SIB myHits motif scan
PRINTS protein fingerprints
SMART - Simple Modular Architecture Research Tool
Blocks WWW Server
Block Search
The Sanger Centre Pfam Server
The Sanger Centre HMM Pfam Searcher
TIGRFAMs protein families HMM
ProDom conserved protein domains
CDD Conserved domains database NCBI
DomCut prediction of linker regions between functional domains
PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System
PIR iProClass Protein Classification
Superfamily HMM models SCOP
Gene3D Structural and Functional Annotation
ModBase - Comparative protein structure models
Interproscan
WebLogo
WebLogo Server
Human Protein Reference Database
PhosphoMotif Finder
ELM Eukaryotic Linear Motif Functional Site Prediction
Phospho.ELM Database of phosphorylation sites
NetworKIN kinase substrate relationship prediction
DIALIGN - multiple sequence alignments to find conserved regulatory elements
The Gibbs Motif Sampler
MEME MAST motif discovery and search

Protein structures

RCSB Protein Data Bank
Entrez-Structure
Conserved Domains Database NCBI
Protein Databank in Europe (PDBe)
Structures by electron microscopy at MSD
SWISS-MODEL
EMBNet - A Quick Guide to Swiss-Model
SCOP: Structural Classification of Proteins
Superfamily HMM models SCOP
CATH database of structural domains
Gene3D Structural and Functional Annotation
The DALI database
NCBI VAST structural alignments
ModBase - Comparative protein structure models
BALL and BALLView Visualization and Modelling Tools

Sequences

Entrez Browser NCBI
SRSWWW EMBL-EBI
DBGET/LinkDB Integrated Database Retrieval System
BCM Search Launcher
GeneCards Weizmann
Genome Matrix databases information integration
RefSeq Reference Sequence NCBI
Unigene NCBI
Uniprot Universal Protein Resource Swiss-Prot/TREMBL/PIR
EMBNet QuickGuide Swissprot Trembl Databases
PIR - Protein Information Resource
IPI - International Protein Index EBI
Human Gene and Protein Database (HGPD)
Protein Identifier Cross-Reference Service
NCBI UniVec and VecScreen Vector contamination search

Genomes

Ensembl Genome Browser
Entrez-Genome NCBI
Integr8 Proteome Analysis at EBI
GOLD: Genomes On Line Database v 3.0
CBS Genome atlas database
MIPS: Munich Information Centre for Protein Sequences
J. Craig Venter Institute (ex TIGR) MD USA
The Sanger Centre
Whitehead Institute
Broad Institute Center for Genome Research
GeneCards Weizmann
HGP - Human genome project information
Human Genome Resources NCBI
Mouse Genome Resources NCBI
Rat Genome resources NCBI
Fugu Fish Genome Project
ZFIN - Zebrafish information network
Wormbase C. elegans
C.elegans Blast server (Sanger Centre)
FlyBase Drosophila
Yeast Genome Database MIPS
Schizosaccharomyces pombe genome (Sanger Centre)
Neurospora crassa Database (Broad)
Neurospora crassa Database (MIPS)
Fungal Genetics Stock Center
tair - The Arabidopsis Information Resource
GABI Primary Database ( GabiPD ) - Genomanalyse Pflanze
Plant genomes (MIPS)
Maize Genetics and Genomic Database
International Rice Genome Sequencing Project
Potato Genome Sequencing Consortium

Bioinformatics server

EBI European Bioinformatics Institute
NCBI US National Center for Biotechnology Information
GenomeNet WWW server Japan
Expasy Proteomics Server
EMBNet - A Quick Guide to Expasy
Pôle Bio-Informatique Lyonnais
Weizmann Institute Bioinformatics and Biological Computing
Baylor College of Medicine HGSC
Bioinformatics Software Server Lille

Link lists

Expasy
Expasy Life Science Directory
Bioinformatics Links Directory UBiC
HSLS: OBRC: Online Bioinformatics Resources Collection
Nucleic Acids Research Database Summary Paper List
Nucleic Acids Research Database Issue 2011
Nucleic Acids Research Database Issue 2010
Nucleic Acids Research Webserver Issue 2011
Nucleic Acids Research Webserver Issue 2010
CMS Molecular Biology Resource
Harvard Dept of MCB - Biology Links
CiteULike - online reference management sharing service
Connotea - online reference and link sharing
del.icio.us social bookmarking
Biotech Europe Link Base

The bioinformatics bench

Linux

Ubuntu Linux
Debian Linux
Open SUSE Linux
Professional SUSE Linux
Fedora Project
RedHat Linux
Linux Kernel Archives
BioLinux - Wikipedia
Knoppix
BioKnoppix
EMBNet A QuickGuide to UNIX
Linux Community (German)
linux.de

WAMP

Apache
SELFHTML
MySQL
PHP
SELFPHP
phpMyAdmin
Comparison of WAMPs
XAMPP

Perl

Perl
The Perl directory at perl.org
Perl documentation
Perl Download
ActiveState - ActivePerl Downloads
Strawberry Perl for Windows
CPAN PERL Script Archiv
Bioperl
Installing Bioperl on Windows - BioPerl
EMBNet QickGuides PERL and Regular Expressions

R and BioConductor

The R project for statistical computing
The Comprehensive R archive network
BioConductor Project - Open Source Software for Bioinformatics
R and Bioconductor Manual (Thomas Girke)
useR! 2011 R user conference Warwick, UK
useR! 2010 R user conference Gaithersburg, Maryland

Editors

The Vim Editor
Proton
Komodo

Laboratory tools

WETLAB: an open source electronic lab notebook
PHP Labware Project
OpenFreezer

EMBOSS

EMBOSS
EMBOSS wiki
EMBOSS application wiki
EMBOSS applications
EMBOSS applications program groups
EMBOSS for Windows
EMBOSS Users Guide
EMBOSS Developers Guide
EMBOSS Administrators Guide
EMBOSS user documentation
EMBOSS FAQ
EMBOSS Main Tutorial
EMBOSS mailing lists
EmbNet EMBOSS and wEMBOSS Quick Guides
JEMBOSS
wEMBOSS
Public SRS installations | Biowisdom

NCBI BLAST software

BLAST Wikipedia
BLAST setup procedure for Windows
NCBI BLAST download
BLAST FASTA databases download
BLAST standalone documentation

Open Source Bioinformatics Platforms

Galaxy bioinformatics framework
myGRID - Open Source Middleware Environment for Bioinformatics Workflows
TAVERNA Open Source Bioinformatics Workbench
eFamily Project - Grid integrating of protein database annotations
Bioclipse - visual platform for structural chemo- and bioinformatics
Systems Biology WorkBench SWB package
Mobyle web environment for bioinformatics workflows
Chinook P2P Bioinformatics Platform
Gaggle data management framework