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Advanced Bioinformatics Frameworks for Molecular Engineering and Protein Analysis

Explore cutting-edge bioinformatics frameworks developed by David Bernick at UC Santa Cruz. This comprehensive overview covers tool integration, file type conversion, and computational services for protein and nucleic acid analysis. Discover resources including the Next Generation Biology Workbench and the ExPASy tools for expert protein analysis. Learn about sequence alignment, visualization techniques, and alignment methods such as ClustalW. Find tutorials and examples to streamline your research in molecular engineering. Enhance your biology workbench experience through various available tools and databases.

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Advanced Bioinformatics Frameworks for Molecular Engineering and Protein Analysis

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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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