The DOI matches its Crossref record; 40 of the 40 references it cites were found in a registry or an index.
DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution
Open accessAbstract
DAMBE is a comprehensive software workbench for data analysis in molecular biology, phylogenetics, and evolution. Several important new functions have been added since version 5 of DAMBE: 1) comprehensive genomic profiling of translation initiation efficiency of different genes in different prokaryotic species, 2) a new index of translation elongation (ITE) that takes into account both tRNA-mediated selection and background mutation on codon-anticodon adaptation, 3) a new and accurate phylogenetic approach based on pairwise alignment only, which is useful for highly divergent sequences from which a reliable multiple sequence alignment is difficult to obtain. Many other functions have been updated and improved including PWM for motif characterization, Gibbs sampler for de novo motif discovery, hidden Markov models for protein secondary structure prediction, self-organizing map for nonlinear clustering of transcriptomic data, comprehensive sequence alignment, and phylogenetic functions. DAMBE features a graphic, user-friendly and intuitive interface, and is freely available from http://dambe.bio.uottawa.ca.
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Cites
EMBOSS: the European molecular biology open software suite.
Rice, P., Longden, I., & Bleasby, A. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(00)02024-2 · Cited by 9,466
Sharp, P. M., & Li, W.-H. (1987) · Nucleic Acids Research · doi:10.1093/nar/15.3.1281 · Cited by 3,992
Shine, J., & Dalgarno, L. (1974) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.71.4.1342 · Cited by 3,621
Vienna RNA secondary structure server
Hofacker, I. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg599 · Cited by 2,345
The ‘effective number of codons’ used in a gene
Wright, F. (1990) · Gene · doi:10.1016/0378-1119(90)90491-9 · Cited by 2,309
Coding-Sequence Determinants of Gene Expression in Escherichia coli
Kudla, G., Murray, A. W., Tollervey, D., & Plotkin, J. B. (2009) · Science · doi:10.1126/science.1170160 · Cited by 1,458
DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution
Xia, X. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst064 · Cited by 1,154
Self-citationThe selection-mutation-drift theory of synonymous codon usage.
Bulmer, M. (1991) · Genetics · doi:10.1093/genetics/129.3.897 · Cited by 1,017
Solving the riddle of codon usage preferences: a test for translational selection
Reis, M. D. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh834 · Cited by 755
Translation efficiency is determined by both codon bias and folding energy
Tuller, T., Waldman, Y. Y., Kupiec, M., & Ruppin, E. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909910107 · Cited by 584 · cited 1×
“Translation initiation is often rate-limiting in bacteria and in bacteriophage (Liljenstrom and von Heijne 1987; Bulmer 1991; Xia 2007c; Xia et al. 2007; Kudla et al. 2009; Tuller et al. 2010; Prabhakaran et al. 2015).”
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Cited by
DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution
Xia, X. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy073 · Cited by 786
Self-citationFarookhi, H., & Xia, X. (2024) · Microorganisms · doi:10.3390/microorganisms12040768 · Cited by 7
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Metadata
- Authors
- Xia, X.
- Venue
- Journal of Heredity
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-04-04
- Volume
- 108
- Issue
- 4
- Pages
- 431-437
- ISSN
- 0022-1503 (ISSN-L)
- 1465-7333
- OpenAlex
- W2604358300
- Cited by
- 401
- References
- 40
- FWCI
- 18.54
- Type
- journal article
- Language
- en
- Open access
- hybrid
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Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
