bio tool frameworks
DESCRIPTION
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 - PowerPoint PPT PresentationTRANSCRIPT
Bio tool frameworks
David BernickBioMolecular 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
Piwi domain in Prokaryotes
Argonaute Protein
QuickTime™ and a decompressor
are needed to see this picture.
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
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 ?