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Introduction to other web-based resources

Introduction to other web-based resources. What? Where? and How? of Bioinformatics June 3, 2009. Protein seq. DNA seq. Protein structure. Protein function. Applications. Bioinformatics.

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Introduction to other web-based resources

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  1. Introduction to other web-based resources What? Where? and How? of Bioinformatics June 3, 2009

  2. Protein seq DNA seq Protein structure Protein function Applications Bioinformatics “Bioinformatics is the application of computer technology to the management and analysis of biological data. The result is that computers are being used to gather, store, analyse and merge biological data.” (http://www.ebi.ac.uk/2can/bioinformatics/bioinf_what_1.html)

  3. Real-life Bioinformatics • Primary Data • Gene or protein sequence • GenBank/EMBL/DDBJ, UniProt • Protein structure • wwPDB • Gene or protein interactions • IntAct, DIP, BioGRID • Functional studies • PubMed • Specialized databases (enzymes >> kinases) • Secondary Data • Protein families • Pfam, Interpro • Protein structure classifications • SCOP, CATH • Protein location, function • GO

  4. Gene name & synonyms Micro-array Data Gene expression Disease/ SNP Gene sequence Protein interactions Protein sequence Protein structure Protein name & synonyms Protein domains Protein function Where do we start?

  5. RCSB links

  6. NCBI links http://www.ncbi.nlm.nih.gov/Sitemap/index.html

  7. NCBI bioinformatics tutorials http://www.ncbi.nlm.nih.gov/Education/index.html

  8. EBI links http://www.ebi.ac.uk/

  9. KEGG links http://www.genome.jp/kegg/kegg2.html

  10. Should I believe all I read/find? • Source of information? (where/who) • Scientific article? • Web-based resource? • Text book or other? • Evidence for the conclusion? (how) • Scientific experiment • Electronic annotation • Based on homology • Sequence • Modeling • Hypothesis/generalization

  11. How to read a scientific paper • Read Abstract • Read Introduction • Read Conclusion / Discussion • Read Methods • Review figures and figure legend • Draw your own conclusion based on data presented • Do you agree with the author’s conclusion? • Read results details

  12. Searching for Lysozyme • My name is Lysozyme. How well do you know me? Independently find all that you can about Lysozyme and make a report.

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