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 ?