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Bio tool frameworks

Bio tool frameworks. David Bernick BioMolecular Engineering UC Santa Cruz. Frameworks. Tool Integration Tool description and links File type conversion File Storage Computational services. Examples. Biology Workbench http://workbench.sdsc.edu Next Generation Biology Workbench

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Bio tool frameworks

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  1. Bio tool frameworks David BernickBioMolecular EngineeringUC Santa Cruz

  2. Frameworks • Tool Integration • Tool description and links • File type conversion • File Storage • Computational services

  3. Examples • Biology Workbench • http://workbench.sdsc.edu • Next Generation Biology Workbench • http://www.ngbw.org • Expasy Tools (Expert Protein Analysis) • http://us.expasy.org • Protein Analysis • NCBI Genome Workbench • http://www.ncbi.nlm.nih.gov/projects/gbench/ • local -- not Web based • sequence analysis

  4. Biology Workbench • San Diego Supercomputer Center • Protein and Nucleic acid • search • alignment • analysis • visualization • common interface • file storage and conversion • tutorials

  5. Next Generation Biology Workbench (Swami) • San Diego Supercomputer Center • Replacement for Biology Workbench

  6. ExPasy tools • Swiss Institute of Bioinformatics • metasite - no file storage • proteins - sequence and structure • Life Science directory

  7. Nucleic acid analysisBiology Workbench • PfAgo - nucleic sequence • TACG - restriction site analysis • Blastn, Blastx • Primer3 • NA stats • SixFrame • RevComp

  8. Usage • 1U04 - pdb structure • Q8U3D2 - UniProt ascension • PF0537 - Systematic name • NP_578266.1 - NCBI protein ascension • We know of relatives in Aquifex aeolicus and Methanocaldococcus jannaschii • We also know that the Piwi domain is detectable. • Is the Methanopyrus kandleri version a 4-domain Argonaute?

  9. Analysis strategy • Protein or DNA sequence? • Data source • What should we look for ? • Search method • Alignment method • Visualization

  10. Piwi domain in Prokaryotes

  11. Argonaute Protein

  12. Analysis • Protein - select PF0537 from UCSC Archaeal Browser • Data source - Non-redundant Protein Database • What should we look for? • include a positive and a negative (4 domain and 3 domain) • Search method - Blastp • Alignment method - ClustalW • Visualization

  13. In class exercises • What is the closest bacterial example of a 4- domain Argonaute ? • (not counting Aquifex aeolicus) • What is the GC content of PF0537 ?

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