Advanced Tutorial: Genomic Search with BLAST

This tutorial was originally developed for Baltic Grid Summer Schoold 2009 by T.Szepieniec et al. and subsequently adapted and improved by Hangi Kim from KISTI/Korea.

Never Born Protein: Genomic Search

Never Born Protein: protein that could exists but are not produced in the nature.

This is an example of real application run on EGEE Grid and described in:

• Never-born proteins: predicting protein structures from your web browser, iSGTW
• G.Minervini et al.: Massive non-natural proteins structure prediction using grid technologies, BMC Bioinformatics 2009, 10(Suppl 6):S22
• Never born proteins as a test case for ab initio protein structures prediction, Bioinformation. 2008; 3(4): 177–179.

• GOAL: Localization of “traces” of selected sequences of proteins in the complete human genome and other species (NCBI). The sequences will be transformed from nucleotide into amino acid sequence (three possible reading frames are planned).
• DATA: large genomic plain text data up to 10 GB
• RESULTS:
  • Tool to quick searching genomic patterns against large dataset.
  • Output data on sequences considered in the project will be interpreted in the aspect of evolution.
• COMPUTATION-SCIENTIST- VIEW: run application that searching patterns against huge database (opportunity of parallelism)

-- JakubMoscicki - 31 Jul 2009