Evidence map›Paper›PMID 41489486›Full record

ArticleGigaScience2026

deMEM: a novel divide-and-conquer framework based on de Bruijn graph for scalable multiple sequence alignment.

Yanming Wei, Zhaoyang Huang, Pinglu Zhang, Yizheng Wang, Yan Li, Liang Yu, Quan Zou

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in GigaScience, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Yanming WeiSchool of Computer Science and Technology, Xidian University, No. 266, Xinglong Section of Xifeng Road, Chang'an Zone, Xi'an, 710126, China.ORCID 0000-0003-4843-3350
Zhaoyang HuangSchool of Computer Science and Technology, Xidian University, No. 266, Xinglong Section of Xifeng Road, Chang'an Zone, Xi'an, 710126, China.ORCID 0009-0005-1546-1437
Pinglu ZhangInstitute of Digital Health, Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, University of Electronic Science and Technology of China, No. 1, Chengdian Road, Kecheng Zone, Quzhou, 324003, China.ORCID 0009-0002-1788-3084
Yizheng WangInstitute of Digital Health, Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, University of Electronic Science and Technology of China, No. 1, Chengdian Road, Kecheng Zone, Quzhou, 324003, China.ORCID 0000-0002-3475-5431
Yan LiSchool of Management, Xi'an Polytechnic University, No.19, Jinhua South Road, Xi'an, 710048, China.
Liang YuSchool of Computer Science and Technology, Xidian University, No. 266, Xinglong Section of Xifeng Road, Chang'an Zone, Xi'an, 710126, China.ORCID 0000-0002-8351-3332
Quan ZouInstitute of Digital Health, Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, University of Electronic Science and Technology of China, No. 1, Chengdian Road, Kecheng Zone, Quzhou, 324003, China.ORCID 0000-0001-6406-1142

Funding

National Natural Science Foundation of China 62452107National Natural Science Foundation of China 62472344Xidian University TZJH2024027
6 · The paper itself

Abstract

backgroundMultiple sequence alignment (MSA) continues to be a central challenge in comparative genomics, where the quality of alignment plays a crucial role in determining the accuracy of downstream analyses. However, the challenge of large-scale alignment remains significant.

findingsThis article introduces deMEM, a novel and effective framework for DNA multiple sequence alignment, which enables existing MSA methods such as MAFFT to handle extremely large sequences. deMEM is a 3-stage alignment process: (i) representing maximum exact matches using a de Bruijn graph and clustering them based on their area, (ii) employing a novel divide-and-conquer framework for alignment, and (iii) providing profile-profile alignment between different clusters.

conclusionsDeMEM enables existing methods like MAFFT to align an extremely large number of sequences, including long sequences that cannot be directly aligned, such as those in a dataset of a thousand monkeypox virus genomes. The deMEM package is free and available at https://github.com/malabz/deMEM.

Indexed as

Computational BiologySequence AlignmentSequence Analysis, DNASoftwareAlgorithmsGenomicsde Bruijn graphmaximum exact matchmultiple sequence alignmentparallel algorithm design

Identifiers

PMID41489486
PMCPMC12878729

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.