ARC FLASH     

Seed Optimisation and Indexing of Genomic Databases      

General
Overview
Intranet
People
Actions
Seed Design
Hardware Synthesis
Application
Contacts
Dominique Lavenier
Partners
Symbiose Project
LIFL bioinfo Group
LESTER lab
LBBMA lab
Related links
ACI ReMIX
West Genopole
      
Overview

Goals

The FLASH project (2006 2007) investigates the optimization of seeds in the context of large genomic database search using BLAST-like algorithms.

Typically, seeds are optimized to reach a better search sensitivity. Here, for a given sensitivity, we want to investigate how seeds can be optimized to reduce the size of the database index.

The FLASH project is related to the ReMIX prototype where a genomic database index is stored on a large FLASH memory. With the rapidely increasing of genomic databases, it is extremely important to manage indexes as small as possible.

Three complementary actions have been proposed:

  1. Theoretical study based on previous works of G. Kucherov and L. Noe to design new seeds;
  2. Test of these new seeds on a real challenging problem;
  3. Improve the ReMIX programming for speeding up the implementation of new reconfigurable operators based on these new seeds.

See the complete proposal (in french).