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

By Vincent Ranwez, Sébastien Harispe, Frédéric Delsuc, Emmanuel J. P. Douzery. PLoS ONE, 2011

676 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b8620a451900817db4003505e6105eea59e424c6

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In Molecular Biology

1. Stephen A. Smith
2. Brent C. Emerson
3. Ya Yang
4. L. Lawson Handley
5. M. Borowiec

Citations in the corpus

• Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics (2014, methodology): “A third approach employed by Agalma (Dunn et al. 2013) uses transcripts translated by all six frames (TBLASTX) for homology search, and then simultaneously translate and align CDS using MACSE (Ranwez et al. 2011).”
• Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring (2012, methodology): “An alternative to MACSE is PyroClean (R. Ramirez-Gonzalez, D. Heavens, M. Caccamo & B.C. Emerson, unpublished), which produces similar results (results not shown).”
• Pitfalls in supermatrix phylogenomics (2017, neutral): “The MACSE program handles such situations by simultaneously considering the nucleotide sequences and their amino-acid translations and by explicitly taking into account frameshift events during the alignment process (Ranwez et al. 2011).”