Bio tool frameworks David Bernick BioMolecular Engineering UC Santa Cruz.
-
Upload
brady-emery -
Category
Documents
-
view
213 -
download
0
Transcript of 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– 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
Biology Workbench
• San Diego Supercomputer Center• Protein and Nucleic acid
– search– alignment– analysis– visualization – common interface– file storage and conversion
• tutorials
Next Generation Biology Workbench (Swami)
• San Diego Supercomputer Center
• Replacement for Biology Workbench
ExPasy tools
• Swiss Institute of Bioinformatics
• metasite - no file storage
• proteins - sequence and structure
• Life Science directory
Nucleic acid analysisBiology Workbench
• PfAgo - nucleic sequence
• TACG - restriction site analysis• Blastn, Blastx• Primer3
• NA stats• SixFrame• RevComp
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?
Analysis strategy
• Protein or DNA sequence?
• Data source
• What should we look for ?
• Search method
• Alignment method
• Visualization
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