UPP2: fast and accurate alignment of datasets with fragmentary sequences.

ABSTRACT:

Motivation

Multiple sequence alignment (MSA) is a basic step in many bioinformatics pipelines. However, achieving highly accurate alignments on large datasets, especially those with sequence length heterogeneity, is a challenging task. Ultra-large multiple sequence alignment using Phylogeny-aware Profiles (UPP) is a method for MSA estimation that builds an ensemble of Hidden Markov Models (eHMM) to represent an estimated alignment on the full-length sequences in the input, and then adds the remaining sequences into the alignment using selected HMMs in the ensemble. Although UPP provides good accuracy, it is computationally intensive on large datasets.

Results

We present UPP2, a direct improvement on UPP. The main advance is a fast technique for selecting HMMs in the ensemble

SUBMITTER: Park M 

PROVIDER: S-EPMC9846425 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature