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Introduction to other web-based resources

Introduction to other web-based resources. What? Where? and How? of Bioinformatics Feb. 19, 2008. 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 Feb. 19, 2008

  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. Bioinformatics Applications • Medicine • Understanding of disease • Drug discovery • Microbial application • Waste cleanup • Improved drugs (antibiotics resistance) • Evolutionary studies • Agriculture • Pest resistance

  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. 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

  6. PDB related resources

  7. NCBI resources

  8. EBI resources

  9. ExPASY resources

  10. Searching for Lysozyme • My name is Lysozyme and I live in Homo sapiens (tax ID ?). How well do you know me? • Clues in • NCBI • BLAST • ENZYME • OMIM • UniProt

  11. Searching for Lysozyme • Name: Lysozyme • Source: Homo sapiens (9606) • Sequence: • Structure: • Location: spleen, lung, kidney, WBC, plasma, saliva, milk, tears • Function: hydrolyse beta(1-4) glycosidic linkages between N-acetylmuramic acid and N-acetylglucosamine of bacterial cell wall; (E.C. 3.2.1.17, 3.2.1.14) • Active site residues: E53, D71 • Disease associations: mutations in gene may cause Renal (and perhaps other) Amyloidosis KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV

  12. 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

  13. 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

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