Team sequoia

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

Section: Scientific Foundations

Sequence processing and Next Generation Sequencing

Sequence algorithms is an established research subject of the team. We have been working on spaced seed techniques for several years and made several contributions, of which one of the most important is the concept of subset seeds  [7] [45] , [46] . The whole technique is implemented and made available in the Yass software for DNA sequence alignment together with the tools implemented to design seeds [10] (see Section  5.1 ). YASS has been used by many researchers and cited in several papers, some of them are mentioned on the YASS website ( ). We have also shown that the proposed seed model was perfectly adapted for protein search  [59] [20] , and we developed such approach in massivelly parallel processing units  [55] . We consider that we gained a good expertise in this area, supported by our theoretical work on algorithmic techniques and data structures.

Members of the team were among the first to work on advanced seeding methods for DNA sequence search [53] , and joined, at early stages, the study of spaced seed design, started in [38] , [49] . The techniques and tools we proposed have been used by the community (see Section  5.1 ) and cited in a number of papers and surveys (e.g. [37] ). Main research groups in the world working on these topics are: Bioinformatics group at Waterloo University (B. Ma, H. Yao, D. Brown, M. Li, B. Brejova, T. Vinar), Departments of Computer Science and Engineering and Genetics at Washington University in St. Louis (J. Buhler, Y. Sun), Department of Computer Science at University of Western Ontario (K. Zhang and L. Ilie), Department of Mathematics at Singapore University (L. Zhang, K. P. Choi, F. Zeng and Y. Kong), Department of Computer Science and Information Engineering at Taiwan University (K.-M. Chao), Department of Computer Science at Ben-Gurion University of the Negev (M. Farach-Colton, G. Landau, S.C. Sahinalp, and D. Tsur), Departments of Biology and Computer Science at Boston University (G. Benson and D.Y. Mak), Center for Bioinformatics and Computational Biology at University of Maryland (L. Zhou and L. Florea).


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