IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) is a quarterly journal that publishes archival research results related to the algorithmic, mathematical, statistical, and computational methods that are central in bioinformatics and computational biology.
Featured Article from the April-June Issue
A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats
By Todd J. Treangen, Aaron E. Darling, Guillaume Achaz, Mark A. Ragan, Xavier Messeguer, and Eduardo P.C. Rocha
Pairwise local sequence alignment methods have been the prevailing technique to identify homologous nucleotides between related species. However, existing methods that identify and align all homologous nucleotides in one or more genomes have suffered from poor scalability and limited accuracy. We propose a novel method that couples a gapped extension heuristic with an efficient filtration method for identifying interspersed repeats in genome sequences. During gapped extension, we use the MUSCLE implementation of progressive global multiple alignment with iterative refinement. The resulting gapped extensions potentially contain alignments of unrelated sequence...
TCBB is a joint publication of the IEEE Computer Society, Association for Computing Machinery, IEEE Computational Intelligence Society, and the IEEE Engineering in Medicine and Biology Society.
Pairwise local sequence alignment methods have been the prevailing technique to identify homologous nucleotides between related species. However, existing methods that identify and align all homologous nucleotides in one or more genomes have suffered from poor scalability and limited accuracy. We propose a novel method that couples a gapped extension heuristic with an efficient filtration method for identifying interspersed repeats in genome sequences. During gapped extension, we use the MUSCLE implementation of progressive global multiple alignment with iterative refinement. The resulting gapped extensions potentially contain alignments of unrelated sequence...
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