Selección de bases de datos, agrupadas por áreas.

Manuel J. Gómez, CNB

Interfaces to multiple databases or Global Databases

SRS6. Sequence Retrieval System, developed in Europe, at the EBI. 
SRS6. Sequence Retrieval System, developed in Europe, at the CNB.
 
DDBJ. DNA Databank of Japan. National Institute of Genetics, Japan. 
EBI - Databases. Databases at the European Bioinformatics Institute, EMBL. 
NCBI. National Center for Biotechnology Information. National Library of Medicine, NIH, US. 

DNA sequences and Genomes

EMBL Nucleotide Sequence and other databases. EBI. 
GenBank. Nucleotide database at NCBI. 
GOLD. Genomes OnLine Database Homepage. 
MOT. Genome Monitoring Table, at EBI. 
EBI Genomes. 
GenoList. Genome Browser at Institut Pasteur. 
GenomeNet. Kyoto University. 
Joint Genome Institute Genome Projects. Department of Energy, US. 
NCBI Genomes 
Sanger Institute Genomes 
TIGR Genomes 
Colibri. Escherichia coli at Institut Pasteur. 
Ensembl. Metazoan genomes at EBI. 
FlyBase. Drosophila Genome Database at Indiana University. 
MGI. Mouse Genome Informatics. The Jackson Laboratory, Maine, US. 
SGD. Saccharomyces Genome Database at Stanford University. 
Subtilist. Bacillus subtilis at Institut Pasteur. 
Tuberculist. Mycobacterium tuberculosis at Institut Pasteur. 
Wormbase. Genome and Biology of C. elegans, at CSHL.

Genome analysis and Comparison

GenomeAtlas. DNA Structural Analysis of Sequenced Microbial Genomes, at CBS. 
GeneQuiz. Automatic analysis of genomes, at EBI. 
HAMAP. High-quality automated and manual annotation of microbial proteomes, at ExPASy. 
INDIGO. Análisis de los genomas de E. coli y B. subtilis 
KEGG. Kyoto Encyclopedia of Genes and Genomes, Kyoto University. 
MBGD. Microbial Genome Database for Comparative Analysis. 
Membrane Transport Systems. Genomic comparisons of membrane transporters. 
PEP. Predictions for Entire Proteomes, at CUBIC. 
PEDANT. Automatic analysis of genomic protein sets, at MIPS. 
WIT. What Is There? Argonne National Laboratory, US.

SNPs

dbSNP Home Page. Single Nucleotide Polymorphism database, at NCBI. 
SNP Consortium. The SNP Consortium, at CSHL.

rRNA and tRNA sequences

Comparative RNA Web Site. Gutell Lab at University of Texas, US. 
Ribosomal Database Project II. Michigan State University, US.

ESTs and cDNAs

dbEST. Expressed Sequence Tags database at NCBI. 
DGC. Drosophila Gene Collection. Full lenght cDNA sequences. 
EST Links. List of links to EST resources, at EBI. 
Human cDNA Projects. MIPS. 
HUNT. Human full-length cDNA sequences. 
MGC. Mammalian Gene Collection. Full lenght cDNA sequences.

Microarray expression data

ArrayExpress. Microarray Expression Data at EBI. 
SMD. Stanford Microarray Database.

Nucleic Acids structure

NDB. Structural information about Nucleic Acids.

Proteins

EMP. Enzymes and Metabolic Pathways, at Argonne National Laboratory, US. 
ENZYME. Enzyme nomenclature database, at ExPASy. 
EXProt. Database for proteins with an experimentally verified function, at CMBI. 
PIR. Protein Information Resource, at Georgetown University. 
Proteome BioKnowledge. Protein knowledge database generated by human experts. 
SWISS-PROT. Curated protein sequence database, at EBI. 
SWISS-PROT and TrEMBL. ExPASy server, Swiss Institute of Bioinformatics. 
TRANSFAC. Transcription Factor Database. 
TrEMBL. Computer annotated, translated EMBL sequences, at EBI. 
Verified Protein Starts. E. coli proteins with verified start.

Protein similarity and Families

CluSTr. SWISS-PROT and TrEMBL proteins classified into groups of related proteins, at EBI. 
COGs. Clusters of Orthologous Groups of proteins, at NCBI. 
InParanoid. Database of pairwise orthologs, at CGB, Karolinska Institute, Sweden. 
ProtoMap. Hierarchical classification of all proteins in SWISSPROT and TrEMBL. 
SYSTERS. Clusters of similar proteins, at CMB, Max Plank Institute.

Patterns, Profiles and Families

Blocks. Multiple alignments of the most highly conserved regions of groups of proteins documented in InterPro. 
InterPro. Integrated view of commonly used motif databases. 
MetaFam Protein Family Database. Comprehensive database of protein family information. 
Pfam: Sanger. Multiple sequence alignments and HMMs of protein domains and families, at Sanger Institute. 
Pfam : Saint Louis 
Pfam: Karolinska 
Pfam INRA 
PRINTS. Database of groups of conserved motifs, or protein fingerprints. 
ProDom. Protein domain families automatically generated from SWISS-PROT and TrEMBL. 
PROSITE. Database of protein families and domains, defined by patterns and profiles, at ExPASy. 
SMART. Simple Modular Architecture Research Tool, at EMBL.

Protein structure and Families

Amino Acid Properties and Structures. Institute of Chemistry, FU, Berlin.. 
Amino Acid Properties and Structures. PROWL, Rockefeller University. 
CATH Database of Structural Domains. Hierarchical classification of protein domain structures 
DSSP. Database of Secondary Structure in Proteins. 
HOMSTRAD. Aligned three-dimensional structures of homologous proteins. 
HSSP. Database of homology-derived secondary structure of proteins. 
FSSP. Fold classification based on Structure-Structure alignment of Proteins. 
OCA. Integrated access to several protein databases. 
PDB. Protein Databank: single international repository for 3-D macromolecular structure data. 
PDBsum. Summaries and structural analyses of PDB data files. 
Protein Loop Classification Index. Computational clustering of loops in the PDB SELECT database. 
RCSB - Databases. Databases of the Research Collaboratory for Structural Bioinformatics, home of PDB. 
SCOP. Structural Classification of Proteins. 
Superfamily. Groups of proteins identified with HMM profiles from superfamilies defined in SCOP. 
TOPS. Protein Topology.

Molecular Interactions

BIND. Biomolecular Interaction Network Database. 
DIP. Database of Interacting Proteins, at UCLA. 
PIMRider. Protein-protein interactions, at Hybrigenics. 
Interact. Protein-Protein Interaction database, at UMBER. 
Molecular Interaction Links. From BIND website.

Metabolism

EMP. Enzymes and Metabolic Pathways at Argonne National Laboratory, US. 
WIT. What Is There?. Argonne National Laboratory, US. 
KEGG. Kyoto Encyclopedia of Genes and Genomes. Kyoto University.

Literature

PubMed. Database of biomedical literature at NCBI.

Gene Ontology

Gene Ontology Consortium. Controlled and hierarchical vocabulary to organize biological knowledge. 
Gene Ontology Annotation. Assignments of gene products to the Gene Ontology, at EBI. 
AmiGO. HTML-based browser for The Gene Ontology. 
Quickgo. Fast web based viewer for the Gene Ontology, et EBI.

Taxonomy

NEWT. Taxonomy database at EBI.. 
Taxonomy Browser. Taxonomy browser at NCBI.

Database lists

DataBase Bookmarks for Bioinformatics. Klaus P. Schafer. University of Konstanz, Germany. 
Deambulum Databank Index. Deambulum, Infobiogen, France. 
Molecular Biology Database Collection: 2003 update. A. D. Baxevanis.