Amino Acid Classification and Hash Seeds for Homology Search
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
MPSCAN: fast localisation of multiple reads in genomes
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Compression, indexing, and retrieval for massive string data
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Design of an efficient out-of-core read alignment algorithm
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Spaced seeds design using perfect rulers
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
Journal of Parallel and Distributed Computing
Accelerating short read mapping on an FPGA (abstract only)
Proceedings of the ACM/SIGDA international symposium on Field Programmable Gate Arrays
Mapping short sequencing reads to distant relatives
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Seed design framework for mapping SOLiD reads
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
An index structure for spaced seed search
ISAAC'11 Proceedings of the 22nd international conference on Algorithms and Computation
Acceleration of the long read mapping on a PC-FPGA architecture (abstract only)
Proceedings of the ACM/SIGDA international symposium on Field programmable gate arrays
Frequency-based re-sequencing tool for short reads on graphics processing units
International Journal of Computational Science and Engineering
Design and analysis of periodic multiple seeds
Theoretical Computer Science
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Motivation: The next generation sequencing technologies are generating billions of short reads daily. Resequencing and personalized medicine need much faster software to map these deep sequencing reads to a reference genome, to identify SNPs or rare transcripts. Results: We present a framework for how full sensitivity mapping can be done in the most efficient way, via spaced seeds. Using the framework, we have developed software called ZOOM, which is able to map the Illumina/Solexa reads of 15× coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity. Availability: ZOOM is freely available to non-commercial users at http://www.bioinfor.com/zoom Contact:bma@csd.uwo.ca, mli@uwaterloo.ca