The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
Open accessAbstract
BACKGROUND: Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N3) in memory. This is only practical for small RNAs. RESULTS: I describe a divide and conquer variant of the alignment algorithm that is analogous to memory-efficient Myers/Miller dynamic programming algorithms for linear sequence alignment. The new algorithm has an O(N2 log N) memory complexity, at the expense of a small constant factor in time. CONCLUSIONS: Optimal ribosomal RNA structural alignments that previously required up to 150 GB of memory now require less than 270 MB.
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Cites
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Cited by
Lorenz, R., Bernhart, S. H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P. F., & Hofacker, I. L. (2011) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-6-26 · Cited by 5,098
Infernal 1.0: inference of RNA alignments
Nawrocki, E. P., Kolbe, D. L., & Eddy, S. R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp157 · Cited by 1,436
Self-citationShukla, S., Mishra, B., Avashthi, H., & Chandra, M. (2022) · Bioinformatics · doi:10.1016/b978-0-323-89775-4.00003-1 · Cited by 1,244
The Ensembl gene annotation system
Aken, B. L., Ayling, S., Barrell, D., Clarke, L., Curwen, V., Fairley, S., Fernandez Banet, J., Billis, K., García Girón, C., Hourlier, T., et al. (2016) · Database · doi:10.1093/database/baw093 · Cited by 1,086
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
Stein, L. D., Bao, Z., Blasiar, D., Blumenthal, T., Brent, M. R., Chen, N., Chinwalla, A., Clarke, L., Clee, C., Coghlan, A., et al. (2003) · PLoS Biology · doi:10.1371/journal.pbio.0000045 · Cited by 940
Metadata
- Authors
- Eddy, S. R.
- Venue
- BMC Bioinformatics
- Published
- 2002-07-02
- Volume
- 3
- Issue
- 1
- Pages
- 18-18
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W2064345118
- Cited by
- 244
- References
- 4
- FWCI
- 3.89
- Type
- journal article
- Language
- en
- Open access
- gold
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