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MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

Author

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  • Vincent Ranwez
  • Sébastien Harispe
  • Frédéric Delsuc
  • Emmanuel J P Douzery

Abstract

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.

Suggested Citation

  • Vincent Ranwez & Sébastien Harispe & Frédéric Delsuc & Emmanuel J P Douzery, 2011. "MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons," PLOS ONE, Public Library of Science, vol. 6(9), pages 1-10, September.
  • Handle: RePEc:plo:pone00:0022594
    DOI: 10.1371/journal.pone.0022594
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    Cited by:

    1. Nicholas A. Levis & Erik J. Ragsdale, 2023. "A histone demethylase links the loss of plasticity to nongenetic inheritance and morphological change," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Rachel A. Steward & Maaike A. de Jong & Vicencio Oostra & Christopher W. Wheat, 2022. "Alternative splicing in seasonal plasticity and the potential for adaptation to environmental change," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    3. Jan Smyčka & Cristina Roquet & Martí Boleda & Adriana Alberti & Frédéric Boyer & Rolland Douzet & Christophe Perrier & Maxime Rome & Jean-Gabriel Valay & France Denoeud & Kristýna Šemberová & Niklaus , 2022. "Tempo and drivers of plant diversification in the European mountain system," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    4. Jun Wang & Meng Wang & Ala Moshiri & R. Alan Harris & Muthuswamy Raveendran & Tracy Nguyen & Soohyun Kim & Laura Young & Keqing Wang & Roger Wiseman & David H. O’Connor & Zach Johnson & Melween Martin, 2024. "Genetic diversity of 1,845 rhesus macaques improves genetic variation interpretation and identifies disease models," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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