Orderly and clear summary of lecture 4 part 1 Data bases and analysis tools from the book "Medical Genomics by Sander Groffen". All the summaries of the lectures match with this book therefore you will easily pass your exam. This will save you a lot of time. I passed this course with an 7,3. Good l...
Medical Genomics – Lecture 4 – Data bases and analysis tools
NIH; National Institutes of Health
NCBI; National Center for Biotechnology Information
NLM; National Library of Medicine
Databases; well-organized collections of data that can be accessed (bereikt) through
the use of query language.
• GenBank; all available protein and nucleotide sequences
• Protein Data Bank; 3D structures of proteins, nucleic acids and carbohydrates
Other important databases; ENA (Euopean nucleotide archive) and DDBJ (DNA
DataBank of Japan). Data exchange occurs daily.
Sequence retrieval (ophalen) systems for users; NCBI, Ensemble, Expasy, DDBJ
etc.
The entrez nucleotide database
NCBI developed entrez nucleotide database.
It is a search and find system. Large scale of data domains, including literature,
nucleotide and protein sequences, complete genomes and 3D structures.
Collection of sequences from;
• GenBank; NIH genetic sequence database, an annotated (van aantekening
voorzien) collection of all publicly DNA sequences
GenBank is part of DDBJ, the European Molecular Biology Laboratory (EMBL)
and GenBank at NCBI.
• RefSeq; collection aims to provide a comprehensive (begrijpelijke), integrated
and non-redundant set of sequences; genomic DNA, transcript (RNA), protein
products. Basis for medical, functional and diversity studies
• PDB (Brookhaven Protein Data Bank); database for 3D structures
The GenBank file format
Locus; locus name, sequence length, molecule type, gen bank division and
modification data
Definition; short description of sequence
Accession; unique identifier for a sequence. (number and letters)
Version; identificationnubmer GI (GenInfo Identifier); parallel to version
Keywords; describe the sequence
Source; where the sequence is from. Short name of the organism.
Organism; scientific name for source organism.
References; Authors that discuss the data
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