Portals and Genome Browsers
Antibodypedia, wiki-based web portal that allows users to share information about antibodies
ArrayExpress, public repository for microarray data
Blast Home Page at NCBI
Cancer Dependency Map - Identifying all dependencies in every cancer cell
cBioPortal for Cancer Genomics. The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets.
DNA Data Bank of Japan DDJB
EMBL-EBI, European Bioinformatics Institute
Ensembl, a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on metazoan genomes.
ExPASy proteomics server of the Swiss Institute for Bioinformatics; access to SWISS-PROT, TrEmBL, other databases and proteomics tools
Genecards, Genecards is a searchable, integrated database of human genes that provides concise genomic related information on all known and predicted human genes.
GenomeNet, Japanese network of database and computational services
National Center for Biotechnology Information (NCBI), gateway to GenBank; Entrez; Pubmed; OMIM; data-mining tools
Nature Protocols Exchange, an open resource where the community of scientists pool their experimental know-how to help accelerate research.
Nuclear Protein Database, searchable database of information on proteins that are localised to the nucleus of vertebrate cells.
Oncomine, web application that integrates and unifies high-throughput cancer profiling data
PSI-Nature Structural Genomics Knowledgebase, free site with which to explore advances in structural biology and structural genomics
Target Validation platform, The Target Validation platform brings together information on the relationships between potential drug targets and diseases.
Model Organism Databases
EcoCyc, database of E. coli genes and metabolism
EuroSCARF, European Saccharomyces cerevisiae Archive for Functional Analysis
FlyBase, database of the Drosophila genome
Mouse Genome Informatics, integrated access to data on the genetics, genomics, and biology of the laboratory mouse, the Jackson laboratory.
PomBase, The scientific resource for fission yeast.
WormBase, the biology and genome of C. elegans
Multiple Alignment Tools
Clustal Omega Clustal Omega is a new multiple alignment sequence program that uses seeded guide trees and HMM profile-profile techniques to generate alignments.
PROMALS, constructs multiple protein sequence alignments using information from database searches and secondary structure prediction.
Proteomics and Protein Sequence Analysis
CBC Prediction Servers Protein Function Analysis
CompPASS Database - Harper Lab Proteomic Database. This site contains all of the IP-MS/MS data from the following papers:
The Human DUB Interactome (Sowa et al., Cell, 2009)
The Human Autophagy Pathway (Behrends et al., Nature, 2010)
The Human ERAD Pathway (Christianson et al., Nature Cell Biology, 2011)
ELM The Eukaryotic Linear Motif resource for Functional Sites in Proteins
Fugue, a fold recognition method using structural environment-specific substitution tables and structure-dependent gap penalties
Integrated Protein Domains InterProScan
NetPhosYeast, predicts serine and threonine phosphorylation sites in yeast proteins.
PaxDb. Protein abundance database.
Phosida, phosphorylation site database. Phosida allows retrieval of phosphorylation data of any protein of interest. It lists phosphorylation sites associated with particular projects and proteomes or, alternatively, displays phosphorylation sites found for any protein or protein group of interest.
Phospho.ELM. A database of S/T/Y phosphorylation sites
Phosphosite, an expert curated knowledgebase of protein phosphorylation
Phyre, Protein Homology/analogY Recognition Engine
PRIDE Archive. The PRIDE PRoteomics IDEntifications (PRIDE) database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence.
ProteomicsDB, proteomics database setup to enable users to explore and analyse human proteome data.
Proteopedia - wiki-based interactive 3D encyclopaedia of proteins and molecules
PSIPRED - protein structure prediction server
Simple Modular Architecture Research Tool (SMART), protein domain finder
STRING - STRING is a database of known and predicted protein interactions.
Protein mutation prediction software
Mutation Taster: A free web-based application to evaluate DNA sequence variants for their disease-causing potential
PPopen: Predicts all possible amino acid subsitutions for a protein of interest
Provean: PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.
SIFT: predicts whether an amino acid substitution affects protein function.
Polyphen2: A tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations.
Yeastmine: an integrated data warehouse for Saccharomyces cerevisiae data as a multi-purpose toolkit.
Whole Genome Analyses
Biogrid. A curated set of physical and genetic interactions.
iHOP, information hyperlinked over proteins
NDEx public server, the Network Data Exchange
TheCellMap.org, a central repository for quantitative genetic interaction data for Saccharomyces cerevisiae
Yeast interactome. A Physical Interactome Map of Saccharomyces Cerevisiae.
DNA repair sites
Bi-specific synthetic lethal DDR shRNA Libraries - The Decipher Project
Genomics of drug sensitivity in cancer, http://www.cancerrxgene.org/
Human Ageing Genomic Resources, a web resource that brings together databases and computational tools to help understand the biology of ageing.
Methods in Enzymology, Volume 408, Page 1-582 (2006) DNA Repair, Part A.
Methods in Enzymology, Volume 409, Page 1-575 (2006) DNA Repair, Part B.