Designing seeds for similarity search in genomic DNA
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Better filtering with gapped q-grams
Fundamenta Informaticae - Special issue on computing patterns in strings
On spaced seeds for similarity search
Discrete Applied Mathematics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Bioinformatics
ZOOM! Zillions of oligos mapped
Bioinformatics
Bioinformatics
Bioinformatics
Bioinformatics
Optimal spaced seeds for hidden Markov models, with application to homologous coding regions
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
CIAA'07 Proceedings of the 12th international conference on Implementation and application of automata
MPSCAN: fast localisation of multiple reads in genomes
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
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The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications We propose a rigorous and flexible algorithmic solution to mapping SOLiD color-space reads to a reference genome The solution relies on an advanced method of seed design that uses a faithful probabilistic model of read matches and, on the other hand, a novel seeding principle especially adapted to read mapping Our method can handle both lossy and lossless frameworks and is able to distinguish, at the level of seed design, between SNPs and reading errors We illustrate our approach by several seed designs and demonstrate their efficiency.