Goals

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).