| External Related Sites |
http://www.123genomics.homestead.com/
- additional site
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| Nucleotide Sequence Databases (the principal ones) |
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NCBI - National Center for Biotechnology Information
EBI - European Bioinformatics Institute
DDBJ - DNA Data Bank of Japa
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| Protein Sequence Databases |
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SWISS-PROT & TrEMBL - Protein sequence database and computer annotated supplement
UniProt - UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository
of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
PIR - Protein Information Resource
MIPS - Munich Information centre for Protein Sequences
HUPO - HUman Proteome Organization
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| Database Searching by Sequence Similarity |
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USC Sequence Alignment Server - align 2 sequences with all possible varieties of dynamic programming
T-COFFEE - multiple sequence alignment
ClustalW @ EBI - multiple sequence alignment
MSA 2.1 - optimal multiple sequence alignment using the Carrillo-Lipman method
BOXSHADE - pretty printing and shading of multiple alignments
Splign - Splign is a utility for computing cDNA-to-Genomic, or spliced sequence alignments. At the heart of the program is a global alignment
algorithm that specifically accounts for introns and splice signals.
Spidey - an mRNA-to-genomic alignment program
SIM4 - a program to align cDNA and genomic DNA
Wise2 - align a protein or profile HMM against genomic sequence to predict a gene structure, and related tools
PipMaker - computes alignments of similar regions in two (long) DNA sequences
VISTA - align + detect conserved regions in long genomic sequences
myGodzilla - align a sequence to its ortholog in the human genome
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| Human Genome Databases |
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| Databases of other Organisms |
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MBGD - comparative analysis of completely sequenced microbial genomes
COGs - phylogenetic classification of orthologous proteins from complete genomes
STRING - detect whether a given query gene occurs repeatedly with certain other genes in potential operons
Pedant - automatic whole genome annotation
GeneCensus - various whole genome comparisons
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| Protein Domains: Databases and Search Tools |
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InterPro - integration of Pfam, PRINTS, PROSITE, SWISS-PROT + TrEMBL
PROSITE - database of protein families and domains
Pfam - alignments and hidden Markov models covering many common protein domains
SMART - analysis of domains in proteins
ProDom - protein domain database
PRINTS Database - groups of conserved motifs used to characterise protein families
Blocks - multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins
Protein Domain Profile Analysis @ BMERC - search a library of profiles with a protein sequence
TIGRFAMs - yet more protein families based on Hidden Markov Models
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| Motif and Pattern Search in Sequences |
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Gibbs Motif Sampler - identification of conserved motifs in DNA or protein sequences
AlignACE Homepage - gene regulatory motif finding
MEME - motif discovery and search in protein and DNA sequences
SAM - tools for creating and using Hidden Markov Models
Pratt - discover patterns in unaligned protein sequences
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| Gene Expression Databases |
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TRAFAC - For identifying conserved and shared cis regulatory elements between a pair of genes.
CisMols - For identifying conserved and shared cis regulatory elements between a set of co-expressed genes.
TRANSFAC - database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors
EPD - eukaryotic promoter database
DBTSS - DataBase of Transcriptional Start Sites (human)
SCPD - Saccharomyces cerevisiae promoter database
DCPD - Drosophila Core Promoter Database
RegulonDB - a database on transcriptional regulation in E. coli
DPInteract - protein binding sites on E. coli DNA
PromoterInspector - prediction of promoter regions in mammalian genomic sequences
MatInspector - search for transcription factor binding sites
Cister - cis-element cluster finder
Gene regulatory Tools
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| Metabolic, Gene Regulatory & Signal Transduction Network Databases |
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KEGG - Kyoto Encyclopedia of Genes and Genomes
BioCarta
DAVID - Database for Annotation, Visualization and Integrated Discovery - A useful server to for annotating microarray and other genetic data.
stke - Signal Transduction Knowledge Environment
BIND - Biomolecular Interaction Network Database
EcoCyc
WIT
SPAD - Signaling Pathway Database
CSNDB - Cell Signalling Networks Database
PathDB
Transpath
DIP - Database of Interacting Proteins
PFBP - Protein Function and Biochemical Networks
Alliance for Cellular Signalling
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| Other Databases (Annotations, Ontologies, Consortia, etc.) |
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Entrez Gene - Gene provides a unified query environment for genes defined by sequence and/or in NCBI's Map Viewer. You can query on names,
symbols, accessions, publications, GO terms, chromosome numbers, E.C. numbers, and many other attributes associated with genes
and the products they encode. Replaces LocusLink.
LocusLink - A single query interface to curated sequence and descriptive information about genetic loci presenting information on official
nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations,
and related web sites.
Cancer Genome Anatomy Project
HUGO's Human Gene Nomenclature
Gene Ontology Consortium - a controlled vocabulary of eukaryotic gene roles
Open Biological Ontologies an umbrella web address for well-structured controlled vocabularies for shared use across different biological domains.
ACUTS - compilation of Ancient Conserved UnTranslated Sequences
UTR database
ENZYME - enzyme nomenclature database
BRENDA - enzyme database
TC-DB - comprehensive classification of membrane transport proteins
The SNP Consortium
HGBASE - database of sequence variations in the human genome
MethDB - DNA methylation database
SpliceDB - canonical and non-canonical splice site sequences in mammalian genes
SpliceOme - database of intron-exon boundaries
InBase - intein database
The I.M.A.G.E. Consortium
The Kabat Database of Sequences of Proteins of Immunological Interest
Nelson Lab: Cytochrome C
REBASE - restriction enzyme database
Chemfinder.com - molecule database
Genomics Institute of the Novartis Research Foundation
Mouse SNPs Database- 670,000+ SNP records, 8.0+ million allele calls. Allele tables are provided by investigators or retrieved from public sources.
All SNPs are mapped to NCBI Mouse Genome build 33 (C57BL/6J assembly). Most are linked to NCBI dbSNP build 123.
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| Computational Resources |
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| Bioinformatics on-line course materials and tutorials (not an exhaustive collection) |
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| Web Sites for Background Information & News |
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| Other Collections of Bioinformatics Resources |
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