The DOI matches its Crossref record; 47 of the 47 references it cites were found in a registry or an index.
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
Open accessAbstract
Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment.We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.MACSE is distributed as an open-source java file executable with freely available source code and can be used via a web interface at: http://mbb.univ-montp2.fr/macse.
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Cites
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Cited by
Leray, M., Yang, J. Y., Meyer, C. P., Mills, S. C., Agudelo, N., Ranwez, V., Boehm, J. T., & Machida, R. J. (2013) · Frontiers in Zoology · doi:10.1186/1742-9994-10-34 · Cited by 1,636
Self-citationBiodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
Yu, D. W., Ji, Y., Emerson, B. C., Wang, X., Ye, C., Yang, C., & Ding, Z. (2012) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2012.00198.x · Cited by 744
MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons
Ranwez, V., Douzery, E. J. P., Cambon, C., Chantret, N., & Delsuc, F. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy159 · Cited by 743
Self-citationReliable, verifiable and efficient monitoring of biodiversity via metabarcoding
Ji, Y., Ashton, L., Pedley, S. M., Edwards, D. P., Tang, Y., Nakamura, A., Kitching, R., Dolman, P. M., Woodcock, P., Edwards, F. A., et al. (2013) · Ecology Letters · doi:10.1111/ele.12162 · Cited by 662
Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts
Gallone, B., Steensels, J., Prahl, T., Soriaga, L., Saels, V., Herrera-Malaver, B., Merlevede, A., Roncoroni, M., Voordeckers, K., Miraglia, L., et al. (2016) · Cell · doi:10.1016/j.cell.2016.08.020 · Cited by 679
Metadata
- Authors
- Ranwez, V., Harispe, S., Delsuc, F., & Douzery, E. J. P.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2011-09-16
- Volume
- 6
- Issue
- 9
- Pages
- e22594
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W1988652743
- Cited by
- 718
- References
- 47
- FWCI
- 6.35
- Type
- journal article
- Language
- en
- Open access
- gold
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