Bioinformatics- The Basics

Frage	Antworten
Bioinformatics	Use of computer science to analyse data
Aim- Organise Data	So it can be accessed and added to by other researchers
Aims- Develop Tools and Resources	To assist in data analysis
Uses- Use Tools to Analyse Data	Use results in a biologically meaningful way
Database	Collection of information stored in a computer
Primary Database	Database of primary data i.e from experiments and curation
Nucleic Acids- Primary Database	Database of nucleic acid sequences
Nucleic Acid Primary Database- Europe	NCBI- 66 million entries and increasing rapidly (different ones for America/Japan)
HGNC	Human Genomic Naming Committee
Protein Sequencing	Database of amino acid sequences of proteins
Protein Sequencing - Primary Database	Uniprot- annotations by 3 schools of PhD students
Protein Sequence- Taxonomic Identifier	Number assigned to each species and its proteins - Humans is 9606
Protein Structure	Database of the 3D structure of proteins (folds etc.)
Protein Structure- Primary Database	Protein Data Bank- sorted by method of attainment
Protein Structure- E.C Number	Enzyme Classification Number
Role of the PDB	To normalise data from different sources
Biographic Databases	Store Original Literature
Secondary Database	Database of classifications derived from primary analysis i.e. protein superfamilies
Secondary Database- TRANSFAC	Superfamilies classified by nuclear sequences
Secondary Database- PFAM	Superfamilies classified by amino acid sequences
Secondary Database- CATH	Superfamilies classified by protein families
Database Problems- Sequencing Errors	Base pairs incorrect/Contaminated DNA/Missing sequences
Database Problems- Names/Data Entry Errors	Multiple names for a single gene/ Same name for 2 genes (common between yeast and humans)
Database Problems- Experimental Data Errors	Hard to detect

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Bioinformatics- The Basics

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