The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
On the Complexity of Multiple Sequence Alignment
Abstract
We study the computational complexity of two popular problems in multiple sequence alignment: multiple alignment with SP-score and multiple tree alignment. It is shown that the first problem is NP-complete and the second is MAX SNP-hard. The complexity of tree alignment with a given phylogeny is also considered.
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Citations
Cites
Optimization, approximation, and complexity classes
Papadimitriou, C. H., & Yannakakis, M. (1991) · Journal of Computer and System Sciences · doi:10.1016/0022-0000(91)90023-x · Cited by 1,653
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Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
Brudno, M., Do, C. B., Cooper, G. M., Kim, M. F., Davydov, E., Program, N. C. S., Green, E. D., Sidow, A., & Batzoglou, S. (2003) · Genome Research · doi:10.1101/gr.926603 · Cited by 1,115
GRANT, T., FROST, D. R., CALDWELL, J. P., GAGLIARDO, R., HADDAD, C. F. B., KOK, P. J. R., MEANS, D. B., NOONAN, B. P., SCHARGEL, W. E., & WHEELER, W. C. (2006) · Bulletin of the American Museum of Natural History · doi:10.1206/0003-0090(2006)299[1:psodfa]2.0.co;2 · Cited by 578
Multiple protein structure alignment at scale with FoldMason
Gilchrist, C. L. M., Mirdita, M., & Steinegger, M. (2026) · Science · doi:10.1126/science.ads6733 · Cited by 117
Biology and medicine in the landscape of quantum advantages
Cordier, B. A., Sawaya, N. P. D., Guerreschi, G. G., & McWeeney, S. K. (2022) · Journal of The Royal Society Interface · doi:10.1098/rsif.2022.0541 · Cited by 87
Multiple genome alignment in the telomere-to-telomere assembly era
Kille, B., Balaji, A., Sedlazeck, F. J., Nute, M., & Treangen, T. J. (2022) · Genome Biology · doi:10.1186/s13059-022-02735-6 · Cited by 47
Detecting differences across multiple instances of code clones
Lin, Y., Xing, Z., Xue, Y., Liu, Y., Peng, X., Sun, J., & Zhao, W. (2014) · Proceedings of the 36th International Conference on Software Engineering · doi:10.1145/2568225.2568298 · Cited by 41
Su, W., Liao, X., Lu, Y., Zou, Q., & Peng, S. (2017) · Journal of Computational Biology · doi:10.1089/cmb.2017.0040 · Cited by 21
Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems?
Mutalova, R., Sarrazin-Gendron, R., Cai, E., Richard, G., Ghasemloo Gheidari, P., Caisse, S., Knight, R., Blanchette, M., Szantner, A., & Waldispühl, J. (2023) · Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems · doi:10.1145/3544548.3581375 · Cited by 6
Player-Guided AI outperforms standard AI in Sequence Alignment Puzzles
Mutalova, R., Sarrazin-Gendron, R., Ghasemloo Gheidari, P., Cai, E., Richard, G., Caisse, S., Knight, R., Blanchette, M., Szantner, A., & Waldispühl, J. (2023) · Proceedings of The ACM Collective Intelligence Conference · doi:10.1145/3582269.3615597 · Cited by 1
“Similar to many classical bioinformatics problems, MSA is known to be NP-hard [38], which means that its computational complexity increases exponentially with the number of sequences to be aligned [38].”
Background
Metadata
- Authors
- WANG, L., & JIANG, T.
- Venue
- Journal of Computational Biology
- Publisher
- SAGE Publications
- Published
- 1994-01
- Volume
- 1
- Issue
- 4
- Pages
- 337-348
- ISSN
- 1066-5277 (ISSN-L)
- 1557-8666
- OpenAlex
- W2002638840
- Cited by
- 934
- References
- 1
- FWCI
- 2.70
- Type
- journal article
- Language
- en
- Open access
- closed
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