Homology and distance measures have been routinely used to compare two biological
sequences, such as proteins or nucleic acids. The homology measure of Needleman and …

The identification of maximally homologous subsequences among sets of long sequences is
an important problem in molecular sequence analysis. The problem is straightforward only …

For the last 20 years, fragment assembly in DNA sequencing followed the “overlap–layout–consensus”
paradigm that is used in all currently available assembly tools. Although this …

Biology is in the midst of a era yielding many significant discoveries and promising many
more. Unique to this era is the exponential growth in the size of information-packed databases. …

Results from physical mapping projects have recently been reported for the genomes of
Escherichia coli, Saccharomyces cerevisiae, and Caenorhabditis elegans, and similar projects …

Some new metrics are introduced to measure the distance between biological sequences,
such as amino acid sequences or nucleotide sequences. These metrics generalize a metric of …

Since the advent of rapid DNA sequencing methods in 1976, scientists have had the problem
of inferring DNA sequences from sequenced fragments. Shotgun sequencing is a well-…

The primary structure of a single-stranded nucleic acid, such as a tRNA, is the sequence of
nucleotides or bases making up the molecule. Secondary structure of such a molecule is a …

The algorithm of Smith & Waterman for identification of maximally similar subsequences is
extended to allow identification of all non-intersecting similar subsequences with similarity …

We develop a dynamic programming algorithm for haplotype block partitioning to minimize
the number of representative single nucleotide polymorphisms (SNPs) required to account for …