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EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment
Open accessPublished version of a preprint
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.
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Metadata
- Authors
- Shen, C., Liu, B., Williams, K. P., & Warnow, T.
- Affiliations
- University of Illinois Urbana-Champaign (US)
- Sandia National Laboratories California (US)
- Corresponding author
- Warnow, Tandy
- Venue
- Algorithms for Molecular Biology
- Published
- 2023-12-07
- Volume
- 18
- Issue
- 1
- Pages
- 21-21
- ISSN
- 1748-7188 (ISSN-L)
- PMC
- PMC10704716
- OpenAlex
- W4389430430
- Cited by
- 5
- References
- 1
- Citations by year
- 2026: 1 · 2025: 3 · 2024: 1
- FWCI
- 0.45
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Algorithms for Molecular Biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- Sandia National Laboratories
- US National Science Foundation (2006069)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Physical Sciences › Mathematics › Theoretical Computer Science › Algorithms and Data Compression
- Keywords
- multiple sequence alignment, Emma, MAFFT, divide-and-conquer, alignment accuracy
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