CREMSA: compressed indexing of (ultra) large multiple sequence alignments.

ABSTRACT:

Motivation

Recent viral outbreaks motivate the systematic collection of pathogenic genomes in order to accelerate their study and monitor the apparition/spread of variants. Due to their limited length and temporal proximity of their sequencing, viral genomes are usually organized, and analyzed as oversized Multiple Sequence Alignments (MSAs). Such MSAs are largely ungapped, and mostly homogeneous on a column-wise level but not at a sequential level due to local variations, hindering the performances of sequential compression algorithms.

Results

In order to enable an efficient handling of MSAs, including subsequent statistical analyses, we introduce CREMSA (Column-wise Run-length Encoding for MSAs), a new index that builds on sparse bitvector representations to compress an ex

SUBMITTER: Salson M 

PROVIDER: S-EPMC12261481 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature