Optimizing Multiple Seeds for Protein Homology Search
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Superiority and complexity of the spaced seeds
SODA '06 Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm
On the complexity of the spaced seeds
Journal of Computer and System Sciences
Superiority of Spaced Seeds for Homology Search
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Computing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Amino Acid Classification and Hash Seeds for Homology Search
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Seed optimization for i.i.d. similarities is no easier than optimal Golomb ruler design
Information Processing Letters
Masking patterns in sequences: A new class of motif discovery with don't cares
Theoretical Computer Science
New algorithms for the spaced seeds
FAW'07 Proceedings of the 1st annual international conference on Frontiers in algorithmics
Gapped extension for local multiple alignment of interspersed DNA repeats
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
A minimum cost process in searching for a set of similar DNA sequences
TELE-INFO'06 Proceedings of the 5th WSEAS international conference on Telecommunications and informatics
Procrastination leads to efficient filtration for local multiple alignment
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
A unifying framework for seed sensitivity and its application to subset seeds
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Fast computation of good multiple spaced seeds
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Probabilistic Arithmetic Automata and Their Applications
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Motivation: Filtration is an important technique used to speed up local alignment as exemplified in the BLAST programs. Recently, Ma et al. discovered that better filtering can be achieved by spacing out the matching positions according to a certain pattern, instead of contiguous positions to trigger a local alignment in their PatternHunter program. Such a match pattern is called a spaced seed. Results: Our numerical computation shows that the ranks of spaced seeds (based on sensitivity) change with the sequences similarity. Since homologous sequences may have diverse similarity, we assess the sensitivity of spaced seeds over a range of similarity levels and present a list of good spaced seeds for facilitating homology search in DNA genomic sequences. We validate that the listed spaced seeds are indeed more sensitive using three arbitrarily chosen pairs of DNA genomic sequences.