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Pattern-induced multi-sequence alignment (PUMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling
Abstract
A multiple sequence alignment algorithm is described that uses a dynamic programming-based pattern construction method to align a set of homologous sequences based on their common pattern of conserved sequence elements. This pattern-induced multi-sequence alignment (PIMA) algorithm can employ secondary-structure dependent gap penalties for use in comparative modelling of new sequences when the three-dimensional structure of one or more members of the same family is known. We show that the use of secondary structure information can significantly improve the accuracy of aligning structure boundaries in a set of homologous sequences even when the structure of only one member of the family is known.
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Cited by
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Katoh, K. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf436 · Cited by 17,027
The netrins define a family of axon outgrowth-promoting proteins homologous to C. elegans UNC-6
Serafini, T., Kennedy, T. E., Gaiko, M. J., Mirzayan, C., Jessell, T. M., & Tessier-Lavigne, M. (1994) · Cell · doi:10.1016/0092-8674(94)90420-0 · Cited by 1,373
A Differential Response of Two Putative Mammalian Circadian Regulators, mper1and mper2, to Light
Albrecht, U., Sun, Z. S., Eichele, G., & Lee, C. C. (1997) · Cell · doi:10.1016/s0092-8674(00)80495-x · Cited by 879
Imataka, H., Gradi, A., & Sonenberg, N. (1998) · The EMBO Journal · doi:10.1093/emboj/17.24.7480 · Cited by 572
Metadata
- Authors
- Smith, R. F., & Smmith, T. F.
- Venue
- "Protein Engineering, Design and Selection"
- Publisher
- Oxford University Press (OUP)
- Published
- 1992
- Volume
- 5
- Issue
- 1
- Pages
- 35-41
- ISSN
- 0269-2139 (ISSN-L)
- 1741-0126
- 1741-0134
- OpenAlex
- W2128442209
- Cited by
- 277
- References
- 0
- FWCI
- 5.73
- Type
- journal article
- Language
- en
- Open access
- closed
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- CoChat. (2026). Citation check: Pattern-induced multi-sequence alignment (PUMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling. https://app.cochat.ai/papers/10.1093/protein/5.1.35
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- Smith, R. F., & Smmith, T. F. (1992). Pattern-induced multi-sequence alignment (PUMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling. "Protein Engineering, Design and Selection". https://doi.org/10.1093/protein/5.1.35
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
