The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Recent developments in the MAFFT multiple sequence alignment program
Abstract
The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics. To rapidly construct a reasonable MSA, we developed the initial version of the MAFFT program in 2002. MSA software is now facing greater challenges in both scalability and accuracy than those of 5 years ago. As increasing amounts of sequence data are being generated by large-scale sequencing projects, scalability is now critical in many situations. The requirement of accuracy has also entered a new stage since the discovery of functional noncoding RNAs (ncRNAs); the secondary structure should be considered for constructing a high-quality alignment of distantly related ncRNAs. To deal with these problems, in 2007, we updated MAFFT to Version 6 with two new techniques: the PartTree algorithm and the Four-way consistency objective function. The former improved the scalability of progressive alignment and the latter improved the accuracy of ncRNA alignment. We review these and other techniques that MAFFT uses and suggest possible future directions of MSA software as a basis of comparative analyses. MAFFT is available at http://align.bmr.kyushu-u.ac.jp/mafft/software/.
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
Improved tools for biological sequence comparison.
Pearson, W. R., & Lipman, D. J. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.8.2444 · Cited by 11,227
Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
Mauve: Multiple alignment of conserved genomic sequence with rearrangements
Darling, A. C. E., Mau, B., Blattner, F. R., & Perna, N. T. (2004) · Genome Research · doi:10.1101/gr.2289704 · Cited by 4,949
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160154 · Cited by 2,960
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
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
Morgenstern, B. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.3.211 · Cited by 678
Alignment Uncertainty and Genomic Analysis
Wong, K. M., Suchard, M. A., & Huelsenbeck, J. P. (2008) · Science · doi:10.1126/science.1151532 · Cited by 411
Cited by
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
Self-citationUCHIME improves sensitivity and speed of chimera detection
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., & Knight, R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr381 · Cited by 15,114
Whole-genome analyses resolve early branches in the tree of life of modern birds
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., et al. (2014) · Science · doi:10.1126/science.1253451 · Cited by 1,901
Human gut microbiota in obesity and after gastric bypass
Zhang, H., DiBaise, J. K., Zuccolo, A., Kudrna, D., Braidotti, M., Yu, Y., Parameswaran, P., Crowell, M. D., Wing, R., Rittmann, B. E., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812600106 · Cited by 1,880
A molecular phylogeny of living primates
Perelman, P., Johnson, W. E., Roos, C., Seuánez, H. N., Horvath, J. E., Moreira, M. A. M., Kessing, B., Pontius, J., Roelke, M., Rumpler, Y., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001342 · Cited by 1,414
“DNA Sequence Analyses Multiple sequence files for each gene segment amplified were aligned by MAFFT version 6 [69,70], imported into Se-Al ver Figure 2.”
Method
Metadata
- Authors
- Katoh, K., & Toh, H.
- Venue
- Briefings in Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-03-27
- Volume
- 9
- Issue
- 4
- Pages
- 286-298
- ISSN
- 1467-5463 (ISSN-L)
- 1477-4054
- OpenAlex
- W2119362018
- Cited by
- 3,586
- References
- 9
- FWCI
- 68.12
- Type
- journal article
- Language
- en
- Open access
- closed
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