Protein Analysis Databases

UCSC Genome Bioinformatics – “contains the reference sequence and working draft assemblies for a large collection of genomes”

EBML-EBI Protein Databases – houses many protein related databases

EBI Integr8 – “deciphered genomes and their corresponding proteomes”

EBI MPsrch – “biological sequence comparison tool”

EBI ClustalW – “multiple sequence alignment program for DNA or proteins”

EBI T-Coffee – “combine results obtained with several alignment methods. For instance if you have an alignment coming from ClustalW2, an other alignment coming from Dialign, and a structural alignment of some of your sequences, T-Coffee will combine all that information and produce a new multiple sequence having the best agreement with all these methods.”

EBI InterProScan Sequence Search – “identifies distant relationships in novel sequences… used for classification of protein sequences”

NCBI Protein BLAST – “finds regions of similarity between biological sequences”
BLink - "Pre-computed sequence alignments, generated from routine all-against-all BLAST comparisons performed at NCBI, are available for each protein record in Entrez. The best 200 of these alignments can be displayed by clicking on the “BLink” link in the upper right-hand corner of Entrez protein reports."

NCBI Conserved Domain Database (CDD) – “used to identify the conserved domains present in a protein query sequence”
 
ExPASy Proteomics Tools
 
Search Tool for the Interacting Genes/Proteins (STRING) – proteins and their interactions
 
Scansite (MIT) – “Scansite works best with standards-compliant browsers, such as Firefox, Mozilla, Netscape, Opera, Galeon, Safari, and Konqueror. Internet Explorer users may have problems and are encouraged to use an alternative.”
 

 DNA Analysis Databases

NetPrimer – primer analysis

Primer3Plus – choose primers for DNA analysis

NEBcutter – “take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once.”

Webcutter – restriction mapping

READSEQ – sequence conversion

Sequence Manipulation Suite –“collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences.”  
 

Genome Browsers

NCBI Map Viewer – “search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest.”

Ensembl Genome Browser – “produces and maintains automatic annotation on selected eukaryotic genomes”

 Protein Information

NCBI Entrez: (select the database from the “Search” drop down box) OR

Protein – protein sequence records

Online Mendelian Inheritance in Man (OMIM) - catalog of human genes and genetic disorders

Molecular Modeling DataBase (MMDB) - "structure database is a subset of three-dimensional structures obtained from the Protein Data Bank excluding theoretical models. MMDB is a database of ASN.1-formatted records, is capable of archiving conventional structural data as well as future descriptions of biomolecules, such as those generated by electron microscopy.”

UniProt – “central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.”

Human Protein Reference Database (HPRD) – “entralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.”
 

Genetic Information

NCBI Entrez:

GenBank – “genetic sequence database, an annotated collection of all publicly available DNA sequences”

RefSeq – “provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products. RefSeq is a baseline for medical, functional, and diversity studies”

Gene – “searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer”

HomoloGene – “system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes”

GeneCards – “includes automatically-mined genomic, proteomic and transcriptomic information, as well as orthologies, disease relationships, SNPs, gene expression, gene function, and service links for ordering assays and antibodies”

ClusterMed – powered by the Vivisimo, it organizes PubMed results into meaningful categories.