MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.

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 premat...

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Autores principales:	Vincent Ranwez, Sébastien Harispe, Frédéric Delsuc, Emmanuel J P Douzery
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6c4f88abd0bc466982100122a80e899f
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spelling	oai:doaj.org-article:6c4f88abd0bc466982100122a80e899f2021-11-04T06:08:26ZMACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.1932-620310.1371/journal.pone.0022594https://doaj.org/article/6c4f88abd0bc466982100122a80e899f2011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21949676/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Until 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.Vincent RanwezSébastien HarispeFrédéric DelsucEmmanuel J P DouzeryPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 9, p e22594 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Vincent Ranwez Sébastien Harispe Frédéric Delsuc Emmanuel J P Douzery MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.
description	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.
format	article
author	Vincent Ranwez Sébastien Harispe Frédéric Delsuc Emmanuel J P Douzery
author_facet	Vincent Ranwez Sébastien Harispe Frédéric Delsuc Emmanuel J P Douzery
author_sort	Vincent Ranwez
title	MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.
title_short	MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.
title_full	MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.
title_fullStr	MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.
title_full_unstemmed	MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.
title_sort	macse: multiple alignment of coding sequences accounting for frameshifts and stop codons.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/6c4f88abd0bc466982100122a80e899f
work_keys_str_mv	AT vincentranwez macsemultiplealignmentofcodingsequencesaccountingforframeshiftsandstopcodons AT sebastienharispe macsemultiplealignmentofcodingsequencesaccountingforframeshiftsandstopcodons AT fredericdelsuc macsemultiplealignmentofcodingsequencesaccountingforframeshiftsandstopcodons AT emmanueljpdouzery macsemultiplealignmentofcodingsequencesaccountingforframeshiftsandstopcodons
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MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.

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