Hardness of optimal spaced seed design (2005)

by François Nicolas , Eric Rivals
Venue:PARK (EDS.), PROCEEDINGS OF THE 16TH ANNUAL SYMPOSIUM ON COMBINATORIAL PATTERN MATCHING (CPM’05)
Citations:17 - 0 self

Active Bibliography

3 Evidence Combination in Hidden Markov Models for Gene Prediction – Bronislava Brejová - 2005
1 Quick, practical selection of effective seeds for homology search – Franco P. Preparata, Louxin Zhang, Kwok Pui Choi - 2005
2 Computing alignment seed sensitivity with probabilistic arithmetic automata – Inke Herms, Sven Rahmann - 2008
38 Improved hit criteria for DNA local alignment – Laurent Noé, Gregory Kucherov - 2004
88 PatternHunter II: Highly Sensitive and Fast Homology Search – Ming Li, Bin Ma, Derek Kisman, John Tromp - 2003
Run Probability of High-Order Seed Patterns and its Applications to Finding Good Transition Seeds – J. L. Yang, L. X. Zhang
A COMPUTATIONAL MODEL OF MOTION PROCESSING IN AREA MST LEARNING TO SEGMENT THREE DIMENSIONAL MOVING OBJECTS – R S Zemel, S J Nowlan, T J Sejnowski
43 A unifying framework for seed sensitivity and its application to subset seeds – Gregory Kucherov, Laurent Noé, Mikhail A. Roytberg - 2006
4 Run probabilities of seed-like patterns and identifying good transition seeds – Jialiang Yang, Louxin Zhang - 2008
2 Amino Acid Classification and Hash Seeds for Homology Search – Weiming Li, Bin Ma, Kaizhong Zhang - 2009
13 A tutorial of recent developments in the seeding of local alignment – Daniel G. Brown, Ming Li, Bin Ma - 2004
SPACED SEEDS FOR CROSS-SPECIES CDNA-TO-GENOME SEQUENCE ALIGNMENT ∗ – Leming Zhou, Ingrid Mihai, Liliana Florea
Efficient alternatives to PSI-BLAST – Michal Startek, Slawomir Lasota, Maciej Sykulski, Anna Gambin, Laurent Noé, Gregory Kucherov - 2012
2 Subset Seed Extension to Protein BLAST – Anna Gambin, Slawomir Lasota, Michal Startek, Maciej Sykulski, Laurent Noé, Gregory Kucherov - 2011
6 Optimal spaced seeds for faster approximate string matching – Martin Farach-Colton, Gad M. Landau, S. Cenk Sahinalp, Dekel Tsur
7 Fast computation of good multiple spaced seeds – Lucian Ilie, Silvana Ilie - 2007
10 Multiple spaced seeds for homology search – Lucian Ilie, Silvana Ilie - 2007
41 Optimizing Multiple Spaced Seeds for Homology Search – Jinbo Xu, Daniel G. Brown, Ming Li, Bin Ma - 2004
27 Superiority and Complexity of the Spaced Seeds – Ming Li, Bin Ma, Louxin Zhang - 2006