Scalable sequence database search using partitioned aggregated Bloom comb trees.

ABSTRACT:

Motivation

The Sequence Read Archive public database has reached 45 petabytes of raw sequences and doubles its nucleotide content every 2 years. Although BLAST-like methods can routinely search for a sequence in a small collection of genomes, making searchable immense public resources accessible is beyond the reach of alignment-based strategies. In recent years, abundant literature tackled the task of finding a sequence in extensive sequence collections using k-mer-based strategies. At present, the most scalable methods are approximate membership query data structures that combine the ability to query small signatures or variants while being scalable to collections up to 10 000 eukaryotic samples. Results. Here, we present PAC, a novel approximate membership query data structure fo

SUBMITTER: Marchet C 

PROVIDER: S-EPMC10311332 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature