The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins
have long been and are still important issues in bioinformatics. To rapidly construct a …

The application of whole-genome shotgun sequencing to microbial communities represents
a major development in metagenomics, the study of uncultured microbes via the tools of …

New genome assemblies have been arriving at a rapidly increasing pace, thanks to
decreases in sequencing costs and improvements in third-generation sequencing …

Whole-genome sequences are now available for many microbial species and clades,
however existing whole-genome alignment methods are limited in their ability to perform …

We have conducted a comprehensive search for conserved elements in vertebrate
genomes, using genome-wide multiple alignments of five vertebrate species (human …

We report the generation and analysis of functional data from multiple, diverse experiments
performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE …

Abstract Comparison of DNA sequences from different species is a fundamental method for
identifying functional elements in genomes. Here, we describe the VISTA family of tools …

Multiple alignment of DNA sequences is an important step in various molecular biological
analyses. As a large amount of sequence data is becoming available through genome and …

Advances in DNA sequencing technology have fueled a rapid increase in the number of
sequenced vertebrate genomes, and we anticipate an explosion in the number of genomes …

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine
and drug development, having made inestimable contributions to human health. We report …