Bio tool frameworks

1
Bio tool frameworks

• David BernickBioMolecular EngineeringUC Santa
  Cruz

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Frameworks

• Tool Integration
• Tool description and links
• File type conversion
• File Storage
• Computational services

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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

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Biology Workbench

• San Diego Supercomputer Center
• Protein and Nucleic acid
• search
• alignment
• analysis
• visualization
• common interface
• file storage and conversion
• tutorials

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Next Generation Biology Workbench (Swami)

• San Diego Supercomputer Center
• Replacement for Biology Workbench

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ExPasy tools

• Swiss Institute of Bioinformatics
• metasite - no file storage
• proteins - sequence and structure
• Life Science directory

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Nucleic acid analysisBiology Workbench

• PfAgo - nucleic sequence
• TACG - restriction site analysis
• Blastn, Blastx
• Primer3
• NA stats
• SixFrame
• RevComp

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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?

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Analysis strategy

• Protein or DNA sequence?
• Data source
• What should we look for ?
• Search method
• Alignment method
• Visualization

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Piwi domain in Prokaryotes
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Argonaute Protein
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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

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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 ?