Title: EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment

Abstract

Abstract Background Adding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with new data, adding sequences into a constraint alignment constructed using biological knowledge, or computing alignments in the presence of sequence length heterogeneity. Although this is a natural problem, only a few tools have been developed to use this information with high fidelity. Results We present EMMA (Extending Multiple alignments using MAFFT--add) for the problem of adding a set of unaligned sequences into a multiple sequence alignment (i.e., a constraint alignment). EMMA builds on MAFFT--add, which is also designed to add sequences into a given constraint alignment. EMMA improves on MAFFT--add methods by using a divide-and-conquer framework to scale its most accurate version, MAFFT-linsi--add, to constraint alignments with many sequences. We show that EMMA has an accuracy advantage over other techniques for adding sequences into alignments under many realistic conditions and can scale to large datasets with high accuracy (hundreds of thousands of sequences). EMMA is available at https://github.com/c5shen/EMMA . Conclusions EMMA is a new tool that provides high accuracy and scalability for adding sequences into an existing alignment.

Authors:

Shen, Chengze; Liu, Baqiao; Williams, Kelly P.; Warnow, Tandy

Publication Date:

Thu Dec 07 00:00:00 EST 2023

Sponsoring Org.:

USDOE

OSTI Identifier:

2229173

Resource Type:

Published Article

Journal Name:

Algorithms for Molecular Biology

Additional Journal Information:

Journal Name: Algorithms for Molecular Biology Journal Volume: 18 Journal Issue: 1; Journal ID: ISSN 1748-7188

Publisher:

Springer Science + Business Media

Country of Publication:

United Kingdom

Language:

English