TY - JOUR
T1 - EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment
AU - Shen, Chengze
AU - Liu, Baqiao
AU - Williams, Kelly P.
AU - Warnow, Tandy
N1 - CS and TW were supported by the US National Science Foundation grant 2006069 (to TW). K.P.W., C.S., and B.L. were supported by the Laboratory Directed Research and Development program at Sandia National Laboratories, which is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia LLC, a wholly-owned subsidiary of Honeywell International Inc. for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
PY - 2023/12
Y1 - 2023/12
N2 - 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.
AB - 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.
KW - Multiple sequence alignment
KW - MAFFT
KW - Constraint alignment
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U2 - 10.1186/s13015-023-00247-x
DO - 10.1186/s13015-023-00247-x
M3 - Article
C2 - 38062452
SN - 1748-7188
VL - 18
JO - Algorithms for Molecular Biology
JF - Algorithms for Molecular Biology
IS - 1
M1 - 21
ER -