Finding All Common Intervals of k Permutations
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Introduction to Algorithms, Third Edition
Introduction to Algorithms, Third Edition
Identifying conserved gene clusters in the presence of orthologous groups
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
An algorithmic view of gene teams
Theoretical Computer Science
Gene Teams with Relaxed Proximity Constraint
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
Hierarchical alignment graph for gene teams finding on whole genomes
Proceedings of the 2007 ACM symposium on Applied computing
Tests for Gene Clusters Satisfying the Generalized Adjacency Criterion
BSB '08 Proceedings of the 3rd Brazilian symposium on Bioinformatics: Advances in Bioinformatics and Computational Biology
Generalized Gene Adjacencies, Graph Bandwidth, and Clusters in Yeast Evolution
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Natural Parameter Values for Generalized Gene Adjacency
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
Finding Nested Common Intervals Efficiently
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
Generalized gene adjacencies, graph bandwidth and clusters in yeast evolution
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Computation of median gene clusters
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
Efficient computation of approximate gene clusters based on reference occurrences
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
A PTAS for the square tiling problem
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
The incompatible desiderata of gene cluster properties
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
Individual gene cluster statistics in noisy maps
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
Integer linear programs for discovering approximate gene clusters
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Gapped permutation patterns for comparative genomics
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Using PQ trees for comparative genomics
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
The statistical significance of max-gap clusters
RCG'04 Proceedings of the 2004 RECOMB international conference on Comparative Genomics
Software note: Gene teams: a new formalization of gene clusters for comparative genomics
Computational Biology and Chemistry
An algorithmic view on multi-related-segments: a unifying model for approximate common interval
TAMC'12 Proceedings of the 9th Annual international conference on Theory and Applications of Models of Computation
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Comparative genomics is a growing field in computational biology, and one of its typical problem is the identification of sets of orthologous genes that have virtually the same function in several genomes. Many different bioinformatics approaches have been proposed to define these groups, often based on the detection of sets of genes that are "not too far" in all genomes. In this paper, we propose a unifying concept, called gene teams, which can be adapted to various notions of distance. We present two algorithms for identifying gene teams formed by n genes placed on m linear chromosomes. The first one runs in O(m2n2) time, and follows a direct and simple approach. The second one is more tricky, but its running time is O(mnlog2(n)). Both algorithms require linear space. We also discuss extensions to circular chromosomes that achieve the same complexity.