1. Bio tool frameworks David Bernick BioMolecular Engineering UC Santa Cruz

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

3. Examples Biology Workbench –http://workbench.sdsc.eduhttp://workbench.sdsc.edu Next Generation Biology Workbench –http://www.ngbw.orghttp://www.ngbw.org Expasy Tools (Expert Protein Analysis) –http://us.expasy.orghttp://us.expasy.org –Protein Analysis NCBI Genome Workbench –http://www.ncbi.nlm.nih.gov/projects/gbench/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 analysis Biology 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 ?