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Bio tool frameworks David Bernick BioMolecular Engineering UC Santa Cruz.

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Presentation on theme: "Bio tool frameworks David Bernick BioMolecular Engineering UC Santa Cruz."— Presentation transcript:

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 PF Systematic name NP_ 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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