ReMIX Project     

A Reconfigurable Memory for Indexing Mass of Data      

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ACI ReMIX
      
Genomic Applications
DNA Database Search

This is the basic and daily task of biologists. GenBank will be indexed in the FLASH memory of ReMIX and query with large DNA sequences.

Intensive Genomic Computation

In cooperation with a INSERM (U693, CHU Angers) biologist team involved in the mitochondrial diseases, ReMIX will be used in the comparison of 400,000 bacterium proteins against various mammal genomes, such as Human, dog, mouse, etc.

Search of repeat sequences into large genomes

A very large part of the genomes are made of repeated sequences. In cooperation with the Jacques Monod Institute, Paris, we are currently investigated a new index scheme to favour extraction of repeated sequences.

Extraction of Maximal Repeat in full genomes

Maximal repeats are particular words from which complex genome structures such as, CRISP or TRANSPOSONS, can be extracted. They can be easily exhibited from a suffix tree build from a full genome. One of the research axe of the ANR modulome project is to map a large suffix tree into the ReMIX FLASH memory for speeding up the maximal repeat extraction.

  contact:

  Dominique Lavenier
  lavenier@irisa.fr

  http://www.irisa.fr/remix