Team sequoia

Overall Objectives
Scientific Foundations
New Results
Contracts and Grants with Industry
Other Grants and Activities

Section: New Results

Sequence processing and Next-Generation Sequencing

Participants : Mathieu Giraud, Marta Girdea, Gregory Kucherov, Laurent Noé.

Next Generation Sequencing

We have started last year a new collaboration with Institut Curie (Paris). We are working on a new method of genome mapping of reads issued from the SOLiD TM sequencing technology. Although there is a number of available software programs for read mapping (ShRiMP, Bowtie, MAQ, PerM, ZOOM, ...), our first results show that we are able to obtain a better performance by using a finer modeling of read coding properties and read qualities. This is done by applying our seed technology, assisted by the Iedera program (see Section  5.1 ). While this work is only in its very beginning, preliminary results have been presented in [29] . It should be developed in the PhD thesis of M. Gîrdea.

We also have continued our experience with parallel sequence filtering methods  [55] , pursuing this direction on NGS: We have recently acquired knowledge of SIMD techniques for fast parallel bandwith alignments that are fruitful on NGS problems.

Runs and palindromes

We continued algorithmic studies on palindromic and periodic structures in words (sequences). In 2009, we proposed a method to exactly count $ \rho$p(n) , the maximal number of runs with period at most p , and provided the first exact limits for some microruns [16] .


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