A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Gapped extension for local multiple alignment of interspersed DNA repeats
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Discrete Applied Mathematics
| Hi-index | 3.84 |
Summary: Chromosomes or other long DNA sequences contain many highly similar repeated sub-sequences. While there are efficient methods for detecting strict repeats or detecting already characterized repeats, there is no software available for detecting approximate repeats in large DNA sequences allowing for weighted substitutions and indels in a coherent statistical framework. Here, we present an implementation of a two-steps method (seed detection followed by their extension) that detects those approximate repeats. Our method is computationally efficient enough to handle large sequences and is flexible enough to account for influencing factors, such as sequence-composition biases both at the seed detection and alignment levels. Availability: http://wwwabi.snv.jussieu.fr/public/RepSeek/ Contact: achaz@abi.snv.jussieu.fr http://www.repetmasker.org