Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems
- D. Sankoff
- 1 October 1985
This work combines the objective functions for alignment (parsimony, or minimal mutations) and folding (free energy), and presents an algorithm which solves all three problems simultaneously for a set of N sequences of length n in time proportional to storage and alignment.
Polyploidy and angiosperm diversification.
Comparisons of diversification rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae, but additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages.
Longest common subsequences of two random sequences
Given two random k-ary sequences of length n, what is f(n,k), the expected length of their longest common subsequence? This problem arises in the study of molecular evolution. We calculate f(n,k) for…
The social correlates and linguistic processes of lexical borrowing and assimilation
This paper represents a comprehensive study of English loanword usage in five diverse francophone neighborhoods in the national capital region of Canada. Twenty thousand loan tokens extracted from…
Minimal Mutation Trees of Sequences
- D. Sankoff
Given a finite tree, some of whose vertices are identified with given finite sequences, we show how to construct sequences for all the remaining vertices simultaneously, so as to minimize the total…
Comparison of musical sequences
Concepts from the theory of sequence comparison are adapted to measure the overall similarity or dissimilarity between two musical scores, and a dynamic programming algorithm is presented for calculating the measure and applied to a set of variations on a theme by Mozart.
Genome rearrangement with gene families
- D. Sankoff
- 1 November 1999
Simulations show that in two random genomes, the expected exemplar distance/n is sensitive to the number and size of gene families, but approaches 1 as the number of singleton families increases, while basing exemplardistance on exemplar reversals distance (ERD), the expected computing cost depends on the configuration of genes but is not sensitive to n.
Macromolecules: the theory and practice of sequence comparison
A mudflap assembly for use with a dump vehicle having dual tires at the rear end thereof and including a pair of flexible flap sections that assures that the attached flap section maintains substantially the same position when the dump body is in the lowered-carry-position or raised-dump-position.
The pineapple genome and the evolution of CAM photosynthesis
The pineapple lineage has transitioned from C3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues, providing the first cis-regulatory link between CAM and circadian clock regulation.
Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.
Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of…