Genetics 875: Websites Used in Course
This is a far-from-comprehensive list of useful genome and proteomic databases. If there are any glaring ommissions, please let us know and we'll add them to the list.
A separate page of partially redundant links in a different formate can be found
here
Organism & Genome Databases
SOURCE : Human, Mouse, Rat gene reports database
WormBase : C. elegans & C. brigsea genome database
FlyBase : Drosophila genome database
Berkeley Drosophila Genome Project (BDGP) : Drosophila genome database
The Arabidopsis Information Resource (TAIR) : Arabidopsis genome database
TIGR Arabidopsis thaliana database
Saccharomyces Genome Database (SGD): Database of yeast genes, info, links
Genolevures : Website of genomic comparisons of Hemisascomycete yeasts
S. pombe GeneDB : S. pombe gene reports database
ASAP (enterobacteria)
E. coli Genome Project
EcoCyc: E. coli K12 database
Other E. coli Links
TIGR-Comprehensive Microbial Resource
Genome Browsers & Tools
UC Santa Cruz (UCSC) Genome Browser : Genome Browser for multiple genomes
Ensemble Genome Browser
VISTA : Genome browser for comparative analysis and phylogenetic footprinting
NCBI Map Viewer : Search genome maps of various organisms
NCBI BLAST
ClustalW : Web-based submission for clustalW multiple alignments
Links to multiple alignment tools
Sequencing Centers & Genome Projects
the Institute for Genomic Research (TIGR)
Sanger Center
Whitehead Institute
Broad Institute
Baylor College
Wash U. Sequencing Center
NCBI Genome Database
Microarray Databases & Datasets
*Note that many microarray publications also note the download source for their data*
NCBI Gene Expression Omnibus (GEO) : repository for raw microarray data from various publications
Stanford Microarray Database (SMD) : repository for raw microarray data and compiled data from various publications
Yale Microarray Database (YMD) : more microarray data
Mega Yeast Dataset : compiled Gasch- and Brown-lab yeast microarray data for hundreds of experiments.
Protein Sequence Information:
SWISS-PROT : Curated protein sequence database
Trembl : Computer-annotated supplement to SWISS-PROT
NCBI Refseq : DNA and protein sequence database
Entrez Protein Database : Compilation of protein sequences from SWISS-PROT, PIR, PRF, PDB
Protein Information Resource (PIR) : Protein sequence database
UniProt : Compilation of protein sequences from Swiss-Prot, TrEMBL, and PIR
Expert Protein Analysis System (Expasy) Tools : Protein analysis and links to other tools and databases
Protein Domain:
Protein Families Database of Alignments and HMMs (Pfam): domain database
Simple Modular Architecture Research Tool (SMART) : protein & domain database
PDB : repository of 3D molecular structures
InterProScan : EMBL/EBI database of proteins and domains
FingerPrintScan : EMBL-EBI search for protein domain matches
EMBL-EBI PPSearch : Search a query protein for motifs and domains
NCBI Conserved Domain Database (CDD) : Search for conserved domains in protein query sequences
Prosite : Database of protein families and domains
Blocks : Database of highly conserved protein domains
Prints : Compendium of protein domain 'fingerprints'
ProDom : protein domain families extracted from SWISS-PROT AND TrEMBL databases
NCBI Cluster of Orthologous Groups of proteins (COG) Database : Database of groups of orthologous proteins
Protein Interaction:
Biomolecular Relations in Information Transmission and Expression (BRITE) : Datbase of binary relations for gene, protein, molecule interactions
Database of Interacting Proteins (DIP) : Catalog of experimentally determined protein interactions
Biomolecular Interactions Network Database (BIND) : Protein interaction database
BioCarta : Pathway and network database
MINT : Experimentally verified protein interactions in mammalian systems
GRID : Protien interaction database for yeast, fly, and worms
Protein-Protein Interaction Database (PPID)
RNAi and Phenotype databases
PhenomicDB
RNAi Database : C. elegans RNAi phenotype database
Synthetic Lethal Analysis by Microarray (SLAM) : Phenotype database of double deletion mutants in yeast
BDGP Drosophila data
Other useful sites and databases
EMBL-EBI : European Bioinformatics Institute biological databases
Tree of Life :
Ontology, GO tools, & motif prediction
Gene Ontology (GO) Consortium: Database of controlled vocabulary for genes and gene products
GoBar : Gene list analysis using gene ontology
FunSpec : Gene list analysis using yeast GO terms
Regulatory Sequence Analysis Tools (RSAT) : Tools for motif prediction and sequence analysis in multiple microbial organisms
Multiple EM for Motif Elicitation (MEME) : EM algorithm for DNA sequence motif prediction