The alignment of sequencing reads against a protein reference database is a major
computational bottleneck in metagenomics and data-intensive evolutionary projects. Although …

We are at the beginning of a genomic revolution in which all known species are planned to
be sequenced. Accessing such data for comparative analyses is crucial in this new age of …

Public databases contain a planetary collection of nucleic acid sequences, but their systematic
exploration has been inhibited by a lack of efficient methods for searching this corpus, …

Background Short-read sequencing technologies have long been the work-horse of
microbiome analysis. Continuing technological advances are making the application of long-read …

Abstract Sequence alignments are the foundations of life science research, but most
innovation so far focuses on optimal alignments, while information derived from suboptimal …

MetaScope is a fast and accurate tool for analyzing (host-associated) metagenome datasets.
Sequence alignment of reads against the host genome (if requested) and against microbial …

The biosphere genomics era is transforming life science research, but existing methods
struggle to efficiently reduce the vast dimensionality of the protein universe. We present …

Background Next Generation Sequencing (NGS) is producing enormous corpuses of short
DNA reads, affecting emerging fields like metagenomics. Protein similarity search--a key step …

Protein–protein interactions (PPIs) play essential roles in most biological processes. The
binding interfaces between interacting proteins impose evolutionary constraints that have …