Portals and Genome Browsers

• AfCS (Alliance for Cell Signalling)-developed RNAi vectors
• Antibodypedia, wiki-based web portal that allows users to share information about antibodies
• ArrayExpress, public repository for microarray data
• ATCC cultures and bioproducts
• Blast Home Page at NCBI
• Bioprotocols, a compendium of searchable protocols.
• Chromatin Structure and Function Webpage
• 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
• FLEXGene, full length expression cDNAs
• 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
• Nature Protocols Exchange, an open resource where the community of scientists pool their experimental know-how to help accelerate research.
• NC160 Cancer Microarray Project, Stanford; a gene expression database for the molecular pharmacology of cancers
• Nucleic Acids Research Methods Online
• 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
• Proteome BioKnowledge Library, access via subscription only
• UCSC Genome Browser

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
• H-Invitational Database, integrated database of the human transcriptome
• mips (Munich Information Center for Protein Sequences), includes comprehensive yeast genome database
• Mouse Genome Informatics, integrated access to data on the genetics, genomics, and biology of the laboratory mouse, the Jackson laboratory.
• Saccharomyces Genome Database
• Schizosaccharomyces pombe GeneDB, This database contains all S. pombe (fission yeast) known and predicted protein coding genes, pseudogenes, transposons, tRNAs, rRNAs, snRNAs, snoRNAs and other known and predicted non-coding RNAs.
• WormBase, the biology and genome of C. elegans

Whole Genome Analyses

• Biogrid. A curated set of physical and genetic interactions.
• ChromatinDB, a web-based application that warehouses genome-wide microarray data mapping patterns of histone modifications and other chromatin features for the model organism Saccharomyces cerevisiae.
• Chromatin Structure and Function Page. Information on chromatin biology, histones and epigenetics -- their impact on biological processes and the researchers that study them.
• E-map. Epistatic-Mini Array Profiles (E-MAP) database.
• iHOP, information hyperlinked over proteins
• miRNA Research Education Centre, offers research synopses on an assortment of miRNA applications coupled with a comprehensive database of peer-reviewed publications.
• Mitocheck, an integrated research project to study the regulation of mitosis in human cells. The project aims to test all human genes for involvement in mitosis by RNAi, then identify a subset which will be studied intensively for changes in phosphorylation, subcellular localization and involvement in protein complexes.
• Pathway Interaction Database, an authoritative database for exploring signaling pathways.
• Yeast interactome. A Physical Interactome Map of Saccharomyces Cerevisiae.

DNA Sequence Analysis

• DNA -> Protein Translator
• ExPasy translation tool
• NCBI ORF Finder
• Primer3. Primer design tool
• Rebase. The restriction enzyme database
• Sequence Analysis wwwTools, a collection of www-links for DNA and protein sequence analysis
• Welcome to Translator

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
• ExPASy Proteomic tools
• 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.
• NPD (Nuclear Protein database) Protein domains. Search the database for proteins containing a given motif or domain.
• The PARP link. A web resource on the PARP protein family and poly(ADP-ribosyl)ation.
• PBIL Sequence Analysis (Pôle Bioinformatique Lyonnais)
• 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
• Protein Functional Analysis resource at EBI
• Protein Families database of alignments and HMMs Pfam
• Proteopedia - wiki-based interactive 3D encyclopaedia of proteins and molecules
• PSIPRED - protein structure prediction server
• Saccharomyces cerevisiae Phosphorylome database.
• Secondary Structure Prediction Methods Wellcome Gateways: Bioresearch
• Simple Modular Architecture Research Tool (SMART), protein domain finder
• SUMOplot, sumoylation site prediction

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.
• T-Coffee

DNA repair sites

• Database of mouse strains carrying targeted mutations in genes affecting biological responses to DNA damage Version 7.
• Human Ageing Genomic Resources, a web resource that brings together databases and computational tools to help understand the biology of ageing.
• Locations of DNA Damage Response and Repair Genes in the Mouse and Correlation with Cancer Risk Modifiers. Electronically accessible database that compares the locations of mouse genes involved in DNA repair, apoptosis, cell cycle and signal transduction with those of known cancer risk modifier genes.
• 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.
• repairGENES. Database of DNA repair genes.
• REPAIRtoire, the first comprehensive database resource for systems biology of DNA damage and repair, Nucleic Acids Research article.
• Review article: Database and Bioinformatics Tools for the Study of DNA Repair

Literature databases

• BioMed Central, open access publisher
• Glossary of Biochemistry and Molecular Biology
• Nature genome gateway, a comprehensive web resource devoted to genomics
• Nucleic Acids Research Database Issue, 2013
• Nucleic Acids Research Web Server Issue, 2012
• PubMed
• Web of Knowledge, web-based service for ISI citation indexes

Other sites of interest

• BlueSci, Cambridge's first popular science magazine
• CellsAlive, a fun site that includes videos of cells growing and dividing
• Cell and Molecular Biology Online, an informational resource for cell and molecular biologists
• European Life Sciences Organization
• GeneClinics, publicly funded medical genetics information resource
• Guide to Internet Resources for Cancer

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