Facing the explosive growth of biological sequence data, such as those of protein/peptide
and DNA/RNA, generated in the post-genomic age, many bioinformatical and mathematical …

With the accomplishment of human genome sequencing, the number of sequence-known
proteins has increased explosively. In contrast, the pace is much slower in determining their …

Abstract The Reference Sequence (RefSeq) project at the National Center for Biotechnology
Information (NCBI) contains nearly 200 000 bacterial and archaeal genomes and 150 …

Asgard is a recently discovered superphylum of archaea that appears to include the closest
archaeal relatives of eukaryotes,,,–. Debate continues as to whether the archaeal ancestor …

The National Center for Biotechnology Information (NCBI) provides a large suite of online
resources for biological information and data, including the GenBank® nucleic acid …

NCBI's CDD, the Conserved Domain Database, enters its 15th year as a public resource for
the annotation of proteins with the location of conserved domain footprints. Going forward …

Despite decades of work by structural biologists, there are still~ 5200 protein families with
unknown structure outside the range of comparative modeling. We show that Rosetta …

Detection of protein homology via sequence similarity has important applications in biology,
from protein structure and function prediction to reconstruction of phylogenies. Although …

Abstract The Basic Local Alignment Search Tool (BLAST) website at the National Center for
Biotechnology (NCBI) is an important resource for searching and aligning sequences. A new …

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have
made important contributions to the theory of sequence database homology search …