Algorithms for sequence analysis via mutagenesis

Algorithms for sequence analysis via mutagenesis

MOTIVATION Despite many successes of conventional DNA sequencing methods, some DNAs remain difficult or impossible to sequence. Unsequenceable regions occur in the genomes of many biologically important organisms, including the human genome. Such regions range in length from tens to millions of bases, and may contain valuable information such as the sequences of important genes. The authors hav...

Efficient Algorithms for Sequence Analysis∗

We consider new algorithms for the solution of many dynamic programming recurrences for sequence comparison and for RNA secondary structure prediction. The techniques upon which the algorithms are based effectively exploit the physical constraints of the problem to derive more efficient methods for sequence analysis.

Novel Algorithms for Protein Sequence Analysis

Ultrafast clustering algorithms for metagenomic sequence analysis

The rapid advances of high-throughput sequencing technologies dramatically prompted metagenomic studies of microbial communities that exist at various environments. Fundamental questions in metagenomics include the identities, composition and dynamics of microbial populations and their functions and interactions. However, the massive quantity and the comprehensive complexity of these sequence d...

Algorithms for Computational Biology: Sequence Analysis

Approximate repeats in genomic sequences are important to identify regions of genomes with similar functionality and understand how they are preserved over time. Previous work on this topic, such as RePuter and Vmatch, was focussed on the fixed error bound version of this problem. The percentage error version has not been effectively tackled yet. Our work tries to give scheme for finding long a...