Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and rep...

Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and represent conserved stretches of columns in the underlying MSA. We introduce Shredtools, which uses mul …

With improvements in sequencing and assembly have come many high-quality telomere-to-telomere assemblies and reference pangenomes. However, the long-read sequencing recipes needed for high quality ass...

Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and rep...

Founded in 1850, The University of Utah is the flagship institution of higher learning in Utah, and offers over 100 undergraduate and more than 90 graduate degree programs to over 30,000 students. Uni...

Openings

Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...

Talk by Ben Langmead - WABI 2025

This version introduces Movi Color. Movi rows are augmented with run colors, defined based on the origin of the suffixes within each run. The Movi Color index can be built by either an additional ...

Pangenome collections are growing to hundreds of high-quality genomes. This necessitates scalable methods for constructing pangenome alignments that can incorporate newly-sequenced assemblies. We prev...

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

Aligning genomes into common coordinates is central to pangenome analysis and construction, but it is also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts ...