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BIOINFORMATICS SOFTWARE TOOLS |
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I. National Center For Biotechnological Information (NCBI)
Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information Entrez—s the integrated, text-based search and retrieval system used at NCBI for the major databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others.
Nucleotide Databases GenBank (dbEST,dbSNP,dbGSS,dbSTS)
Protein Databases
Structure Databases
Genomes Databases
Expression Databases GEO (Gene Expression Omnibus) Profiles
Taxonomy Databases
OMIM (Online Mendelian Inheritance In Man)
European Bioinformatics Institute (EBI) The main missions of the European Bioinformatics Institute (EBI) centre on building, maintaining and providing biological databases and information services to support data deposition and exploitation.
UniProt Knowledgebase - a complete annotated protein sequence database Macromolecular Structure Database - European Project for the management and distribution of data on macromolecular structures ArrayExpress - for gene expression data Ensembl - Providing up to date completed metazoic genomes and the best possible automatic annotation. IntAct - Provides a freely available, open source database system and analysis tools for protein interaction data.
DDBJ is the sole DNA data bank in Japan, which is officially certified to collect DNA sequences from researchers and to issue the internationally recognized accession number to data submitters. DDBJ collect data mainly from Japanese researchers, but of course accept data and issue the accession number to researchers in any other countries. Since we exchange the collected data with EMBL/EBI and GenBank/NCBI on a daily basis, the three data banks share virtually the same data at any given time. PROTEIN DATA BANK - The single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.” The PDB includes 10132 coordinate entries, 9422 proteins, 698 nucleic acids, and12 carbohydrates. PROSITE - A database of protein families and domains. It is produced by and is closely linked to the ExPasy site, which hosts the Swiss-Prot sequence database. UniProt - The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information PIR Protein Sequence Database - The database is described by its sponsor as “functionally annotated protein sequences, which grew out of the Atlas of Protein Sequence and Structure (1965-1978) edited by Margaret Dayhoff and has been incorporated into an integrated knowledge base system of value-added databases and analytical tools.” From the Protein Information Resource, the major U.S. source of protein informatics. Swiss-Prot - The major European protein sequence database, with accompanying annotations, from the Swiss Institute of Bioinformatics. “Swiss-Prot is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases.” Also at this site is TrEMBL, which contains all translated nucleic acid protein coding sequences in EMBL that have not yet been annotated and incorporated into Swiss-Prot. Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. For each family in Pfam you can: Look at multiple alignments, View protein domain architectures, Examine species distribution, Follow links to other databases, View known protein structures. |
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Bioinformatics Databases |