Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Journal of the ACM (JACM)
Gossip is synteny: incomplete gossip and an exact algorithm for syntenic distance
SODA '01 Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms
Gossip is synteny: incomplete gossip and the syntenic distance between genomes
Journal of Algorithms
Reconstructing an ancestral genome using minimum segments duplications and reversals
Journal of Computer and System Sciences - Computational biology 2002
(1 + ɛ)-Approximation of sorting by reversals and transpositions
Theoretical Computer Science
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
WADS '01 Proceedings of the 7th International Workshop on Algorithms and Data Structures
Permutation Editing and Matching via Embeddings
ICALP '01 Proceedings of the 28th International Colloquium on Automata, Languages and Programming,
Sorting by Prefix Transpositions
SPIRE 2002 Proceedings of the 9th International Symposium on String Processing and Information Retrieval
Structural Properties and Tractability Results for Linear Synteny
COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
Edit Distance with Move Operations
CPM '02 Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching
Simple and Practical Sequence Nearest Neighbors with Block Operations
CPM '02 Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching
(1+epsilon)-Approximation of Sorting by Reversals and Transpositions
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
A new approximation algorithm for sorting of signed permutations
Journal of Computer Science and Technology
On maximal instances for the original syntenic distance
Theoretical Computer Science
A 1.5-approximation algorithm for sorting by transpositions and transreversals
Journal of Computer and System Sciences - Special issue on bioinformatics II
Pattern matching with address errors: rearrangement distances
SODA '06 Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm
A simpler and faster 1.5-approximation algorithm for sorting by transpositions
Information and Computation
New Bounds and Tractable Instances for the Transposition Distance
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A 1.375-Approximation Algorithm for Sorting by Transpositions
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Reversal and transposition medians
Theoretical Computer Science
Edit distance with move operations
Journal of Discrete Algorithms
Faster algorithms for sorting by transpositions and sorting by block interchanges
ACM Transactions on Algorithms (TALG)
Whole genome duplications, multi-break rearrangements, and genome halving problem
SODA '07 Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms
Sorting by transpositions: dealing with length-weighted models
International Journal of Bioinformatics Research and Applications
Multi-break rearrangements and chromosomal evolution
Theoretical Computer Science
An approximation algorithm for sorting by reversals and transpositions
Journal of Discrete Algorithms
Expected number of breakpoints after t random reversals in genomes with duplicate genes
Discrete Applied Mathematics
Approximate String Matching with Address Bit Errors
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
A 2.25-Approximation Algorithm for Cut-and-Paste Sorting of Unsigned Circular Permutations
COCOON '08 Proceedings of the 14th annual international conference on Computing and Combinatorics
On the Toric Graph as a Tool to Handle the Problem of Sorting by Transpositions
BSB '08 Proceedings of the 3rd Brazilian symposium on Bioinformatics: Advances in Bioinformatics and Computational Biology
Transposition Distance Based on the Algebraic Formalism
BSB '08 Proceedings of the 3rd Brazilian symposium on Bioinformatics: Advances in Bioinformatics and Computational Biology
Edit Distances and Factorisations of Even Permutations
ESA '08 Proceedings of the 16th annual European symposium on Algorithms
Interchange Rearrangement: The Element-Cost Model
SPIRE '08 Proceedings of the 15th International Symposium on String Processing and Information Retrieval
A quadratic time 2-approximation algorithm for block sorting
Theoretical Computer Science
Block sorting: a characterization and some heuristics
Nordic Journal of Computing
Pattern matching with address errors: Rearrangement distances
Journal of Computer and System Sciences
Finding All Sorting Tandem Duplication Random Loss Operations
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Interchange rearrangement: The element-cost model
Theoretical Computer Science
Efficient computations of l1 and l∞ rearrangement distances
Theoretical Computer Science
Constraint Programming Models for Transposition Distance Problem
BSB '09 Proceedings of the 4th Brazilian Symposium on Bioinformatics: Advances in Bioinformatics and Computational Biology
Genome rearrangement and planning
AAAI'05 Proceedings of the 20th national conference on Artificial intelligence - Volume 3
Approximate string matching with address bit errors
Theoretical Computer Science
A simpler and faster 1.5-approximation algorithm for sorting by transpositions
Information and Computation
Extending Bafna-Pevzner algorithm
ISB '10 Proceedings of the International Symposium on Biocomputing
An improved algorithm for sorting by block-interchanges based on permutation groups
Information Processing Letters
A simpler 1.5-approximation algorithm for sorting by transpositions
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
On the similarity of sets of permutations and its applications to genome comparison
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
Signed genome rearrangement by reversals and transpositions: models and approximations
COCOON'99 Proceedings of the 5th annual international conference on Computing and combinatorics
Multi-break rearrangements: from circular to linear genomes
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
Recovering true rearrangement events on phylogenetic trees
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
On the cost of interchange rearrangement in strings
ESA'07 Proceedings of the 15th annual European conference on Algorithms
Efficient computations of l1and l∞rearrangement distances
SPIRE'07 Proceedings of the 14th international conference on String processing and information retrieval
Genome rearrangement algorithms for unsigned permutations with O(log n) singletons
TAMC'08 Proceedings of the 5th international conference on Theory and applications of models of computation
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
An improved 1.375-approximation algorithm for the transposition distance problem
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Cycle detection and correction
ICALP'10 Proceedings of the 37th international colloquium conference on Automata, languages and programming
Bounds on the transposition distance for lonely permutations
BSB'10 Proceedings of the Advances in bioinformatics and computational biology, and 5th Brazilian conference on Bioinformatics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Approximate string matching with stuck address bits
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
The transposition median problem is NP-complete
Theoretical Computer Science
Sorting unsigned permutations by weighted reversals, transpositions, and transreversals
Journal of Computer Science and Technology
On the Cost of Interchange Rearrangement in Strings
SIAM Journal on Computing
Unitary Toric Classes, the Reality and Desire Diagram, and Sorting by Transpositions
SIAM Journal on Discrete Mathematics
Approximate string matching with stuck address bits
Theoretical Computer Science
Discrete Applied Mathematics
Sorting by transpositions is difficult
ICALP'11 Proceedings of the 38th international colloquim conference on Automata, languages and programming - Volume Part I
Analysis and implementation of sorting by transpositions using permutation trees
BSB'11 Proceedings of the 6th Brazilian conference on Advances in bioinformatics and computational biology
Transposition Rearrangement: Linear Algorithm for Length-Cost Model
Annales UMCS, Informatica
Transposition Rearrangement: Linear Algorithm for Length-Cost Model
Annales UMCS, Informatica
A Lower Bound on the Transposition Diameter
SIAM Journal on Discrete Mathematics
Maximizing synteny blocks to identify ancestral homologs
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
Efficient sampling of transpositions and inverted transpositions for bayesian MCMC
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
A 2-approximation algorithm for sorting by prefix reversals
ESA'05 Proceedings of the 13th annual European conference on Algorithms
Matrix tightness: a linear-algebraic framework for sorting by transpositions
SPIRE'06 Proceedings of the 13th international conference on String Processing and Information Retrieval
Faster algorithms for sorting by transpositions and sorting by block-interchanges
TAMC'06 Proceedings of the Third international conference on Theory and Applications of Models of Computation
The streaming complexity of cycle counting, sorting by reversals, and other problems
Proceedings of the twenty-second annual ACM-SIAM symposium on Discrete Algorithms
Bounding prefix transposition distance for strings and permutations
Theoretical Computer Science
A 1.375-approximation algorithm for sorting by transpositions
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
A new tight upper bound on the transposition distance
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
A faster and simpler 2-approximation algorithm for block sorting
FCT'05 Proceedings of the 15th international conference on Fundamentals of Computation Theory
String rearrangement metrics: a survey
Algorithms and Applications
A new approximation algorithm for cut-and-paste sorting of unsigned circular permutations
Journal of Computer and System Sciences
The 1.375 approximation algorithm for sorting by transpositions can run in O(n log n) time
WALCOM'10 Proceedings of the 4th international conference on Algorithms and Computation
Genome rearrangement in mitochondria and its computational biology
RCG'04 Proceedings of the 2004 RECOMB international conference on Comparative Genomics
Sorting by weighted reversals, transpositions, and inverted transpositions
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
A (1+ε)-approximation algorithm for sorting by short block-moves
Theoretical Computer Science
Cycle detection and correction
ACM Transactions on Algorithms (TALG)
A new and faster method of sorting by transpositions
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
Approximate period detection and correction
SPIRE'12 Proceedings of the 19th international conference on String Processing and Information Retrieval
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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Sequence comparison in computational molecular biology is a powerful tool for deriving evolutionary and functional relationships between genes. However, classical alignment algorithms handle only local mutations (i.e., insertions, deletions, and substitutions of nucleotides) and ignore global rearrangements (i.e., inversions and transpositions of long fragments). As a result, the applications of sequence alignment to analyze highly rearranged genomes (i.e., herpes viruses or plant mitochondrial DNA) are rather limited. The paper addresses the problem of genome comparison versus classical gene comparison and presents algorithms to analyze rearrangements in genomes evolving by transpositions. In the simplest form the problem corresponds to sorting by transpositions, i.e., sorting of an array using transpositions of arbitrary fragments. We derive lower bounds on {\em transposition distance} between permutations and present approximation algorithms for sorting by transpositions. The algorithms also imply a nontrivial upper bound on the transposition diameter of the symmetric group. Finally, we formulate two biological problems in genome rearrangements and describe the first {\em algorithmic} steps toward their solution.