Introduction to algorithms
Large scale sequencing by hybridization
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Computation and Visualization of Degenerate Repeats in Complete Genomes
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Correcting Base-Assignment Errors in Repeat Regions of Shotgun Assembly
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Detecting Repeat Families in Incompletely Sequenced Genomes
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Correcting short reads with high error rates for improved sequencing result
International Journal of Bioinformatics Research and Applications
Ab initio whole genome shotgun assembly with mated short reads
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
Computability of models for sequence assembly
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Efficient bubble enumeration in directed graphs
SPIRE'12 Proceedings of the 19th international conference on String Processing and Information Retrieval
| Hi-index | 0.00 |
Repetitive sequences make up a significant fraction of almost any genome and an important and still open question in bioinformatics is how to represent all repeats in DNA sequences. We propose a radically new approach to repeat classification that is motivated by the fundamental topological notion of quotient spaces. A torus or Klein bottle are examples of quotient spaces that can be obtained from a square by gluing some points. Our new repeat classification algorithm is based on the observation that the alignment-induced quotient space of a DNA sequence compactly represents all sequence repeats. This observation leads to a simple and efficient solution of the repeat classification problem as well as new approaches to fragment assembly and multiple alignment.