Skip lists: a probabilistic alternative to balanced trees
Communications of the ACM
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Efficient string matching: an aid to bibliographic search
Communications of the ACM
A linear space algorithm for computing maximal common subsequences
Communications of the ACM
Communications of the ACM
Computation and Visualization of Degenerate Repeats in Complete Genomes
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
The Conserved Exon Method for Gene Finding
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
EMAGEN: an efficient approach to multiple whole genome alignment
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
Extension and use of KMRCRelat algorithm for biological problems
Journal of Computational Methods in Sciences and Engineering - Selected papers from the International Conference on Computer Science, Software Engineering, Information Technology, e-Business, and Applications, 2004
A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Pairwise sequence alignment algorithms: a survey
Proceedings of the 2009 conference on Information Science, Technology and Applications
GAME: A simple and efficient whole genome alignment method using maximal exact match filtering
Computational Biology and Chemistry
The solution space of genome sequence alignment and LIS graph decomposition
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Multiple genome alignment based on longest path in directed acyclic graphs
International Journal of Bioinformatics Research and Applications
Procrastination leads to efficient filtration for local multiple alignment
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Improved genetic algorithm for multiple sequence alignment using segment profiles (GASP)
ADMA'06 Proceedings of the Second international conference on Advanced Data Mining and Applications
An automata approach to match gapped sequence tags against protein database
CIAA'04 Proceedings of the 9th international conference on Implementation and Application of Automata
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Comparative analysis of syntenic genome sequences can be used to identify functional sites such as exons and regulatory elements. Here, the first step is to align two or several evolutionary related sequences and, in recent years, a number of computer programs have been developed for alignment of large genomic sequences. Some of these programs are extremely fast but often time-efficiency is achieved at the expenese of sensitivity. One way of combining speed and sensitivity is to use an anchored-alignment approach. In a first step, a fast heuristic identifies a chain of strong sequence similarities that serve as anchor points. Ina second step, regions between these anchor points are aligned using a slower but more sensitive method.We present CHAOS, a novel algorithm for rapid identification of chains of local sequence similarities among large genomic sequences. Similarities identified by CHAOS are used as anchor points to improve the running time of the DIALIGN alignment program. Systematic test runs show that this method can reduce the running time of DIALIGN by more than 93% while affecting the quality of the resulting alignments by only 1%.The source code for CHAOS is available at http://www.stanford.edu/~brudno/chaos/An integrated program package containing CHAOS and DIALIGN is available at http://bibiserv.techfak.uni-bielefeld.de/dialign/