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Bioinformatics growth curves

Bioinformatics growth curves. Medline records Computer power DNA sequences 3-D structures. Database searching. Text or sequence? Syntax Results Links to other resources. Problems. Amount of data Different formats Lack of annotation Links between databases

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Bioinformatics growth curves

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  1. Bioinformatics growth curves • Medline records • Computer power • DNA sequences • 3-D structures

  2. Database searching • Text or sequence? • Syntax • Results • Links to other resources

  3. Problems • Amount of data • Different formats • Lack of annotation • Links between databases • Quality (e.g. unfinished sequence) • Keeping up to date

  4. DNA and protein databases • Genbank (DNA) • EMBL (DNA) • Swissprot - fully annotated, so delays in things appearing • SCOP - Structural Classification of Proteins • OWL - non-redundant protein database - can be found at HGMP website

  5. Search concepts • Boolean search - combine terms with AND, NOT, OR. Default is usually AND. • Broadening or narrowing search if too few or too many results • Proximity search - place quotes round words to specify a phrase • Wild cards. Hemo* finds hemoglobin, hemophilus, etc.

  6. Entrez • Available from NCBI • Easy to use • Sequence databases, Medline, taxonomy • Batch mode to download and work on large datasets • Search, review results, add terms to refine search

  7. Sequence retrieval system (SRS) • Available from EBI • Interface to >80 databases • Searching/saving results • Links to other databases and launch Blast, ClustalW • Online help for advanced features • Very powerful, needs learning

  8. Human Gene Mutation Available at UWCM Mutations in human genes (mostly disease-related) OMIM Available at HGMP Easy to use - like a big searchable book Definitive clinical genetic information Medical genetics databases

  9. Genome sequence browsers • Several labs and websites, different formats • Example in UK is Ensembl • “The Golden Path” (UCSC) is my favourite • All human (and other) genome sequence, annotated • Easy to get various types of map • Various ways of searching the database

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