Many basic tasks in computational biology involve operations on individual DNA and protein sequences. These sequences, even when anonymized, are vulnerable to re-identification a...
COMPASS is a method for homology detection and local alignment construction based on the comparison of multiple sequence alignments (MSAs). The method derives numerical profiles f...
Ruslan Sadreyev, Ming Tang, Bong-Hyun Kim, Nick V....
Abstract. The rapidly emerging field of metagenomics seeks to examine the genomic content of communities of organisms to understand their roles and interactions in an ecosystem. I...
Gianluigi Folino, Fabio Gori, Mike S. M. Jetten, E...
Background: Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algo...
Background: Sequence comparisons make use of a one-letter representation for amino acids, the necessary quantitative information being supplied by the substitution matrices. This ...