Biological Databases and Bioinformatics Resources

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NetPath is a manually curated resource of human signal transduction pathways.
Reactome is a navigable map of human biological pathways, ranging from metabolic processes (metabolic pathways) to hormonal signalling (signal transduction pathways).

The ProDom database contains protein domain families generated from the UniProtKB database by automated sequence comparisons.

Correct answer. FASTA is a DNA and protein sequence alignment software package.

Correct answer. Secondary databases contain results from the analysis of sequences in the primary databases. Examples of secondary databases are PROSITE and Pfam.

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ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.
PROSITE is a protein database consisting of entries describing the protein families, domains and functional sites as well as amino acid patterns and profiles in them.

Correct answer. Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.

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The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein and genetic interactions.
STRING is a database of known and predicted protein interactions.

Correct answer. The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein and genetic interactions.

Correct answer. VectorBase is an NIAID Bioinformatics Resource Center dedicated to providing data to the scientific community for Invertebrate Vectors of Human Pathogens.

Correct answer. Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database.

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BRAEMBL, pronounced "bramble", is a research support facility for bioinformatics services at the University of Queensland.
The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated DNA and RNA sequences produced and maintained by the European Bioinformatics Institute.
The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan.
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations produced and maintained by the National Center for Biotechnology Information (NCBI).

Correct answer. TreeFam is a database of evolutionary trees of animal genes which aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families.

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The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. It consists of the following databases: DNA Data Bank of Japan (Japan), GenBank (USA) and the European Nucleotide Archive (UK).

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The PROSITE dictionary of sites and patterns in proteins is prepared by Amos Bairoch at the University of Geneva.
The X-ray crystallography Protein Data Bank (PDB) is compiled at the Brookhaven National Laboratory.
Online Mendelian Inheritance in Man (OMIM) data bank is prepared by Victor Mc Kusick, Claire A. Francomano and Stylianos E. Antonarakis at John Hopkins University.

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DNA Data Bank of Japan (DDBJ) is a nucleotide sequence database. It is a biological database that collects DNA sequences.
MEDLINE is a bibliographic database of life sciences and biomedical information which provides bibliographic information for articles from academic journals covering medicine, nursing, pharmacy, dentistry, veterinary medicine and health care.
NatureServe is a sophisticated biodiversity database which acts as an authoritative source for information on more than 70,000 plants, animals and ecosystems of the United States and Canada.
WormBase is an online biological database about the biology and genome of the model organism Caenorhabditis elegans (a nematode) and contains information about other related nematodes.