RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

By Rasmus Wernersson, Anders Gorm Pedersen. Nucleic Acids Res., 2003

522 citations recorded by the source corpus.

Subfields: Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/eee767c0a2a0b268541d85c06b75dba4a60dde75

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

In Pharmacology

Citations in the corpus

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons (2011, methodology): “Ignoring the AA translation is a major handicap in these methods for two main reasons [18,19]: (i) as NT sequences are less conserved, clear similarities at the AA level can be obscured at the NT level thus complicating the alignment; (ii) current optimization criteria during the alignment…”
Complete nucleotide sequence and organization of the mitogenome of endangered Eumenis autonoe (Lepidoptera: Nymphalidae) (2010, background): “1.4 (Wernersson and Pedersen, 2003), which aligns coding sequences on the basis of protein alignments.”
Developmental Gene Evolution and the Origin of Grass Inflorescence Diversity (2006, methodology): “Nucleotide sequences were aligned, based on the conceptual amino acid translation, using RevTrans (Wernersson and Pedersen, 2003) or a combination of CLUSTALX and MacClade 4 (Maddison and Maddison, 2003), before being adjusted manually using MacClade 4.”
ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. (2012, methodology): “Several tools have been developed to automate back-translated nucleotide alignments of protein-coding sequences [11–15].”
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations (2010, methodology): “All these solutions, with the exception of RevTrans, require that the user provide the amino acid alignment together with nucleotide sequences, some of the packages do not provide a complete list of available genetic codes (PAL2NAL) and, except for protal2dna, none of these tools allows the user to ”
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments (2006, background): “In the ideal case where the protein and the corresponding DNA match perfectly, the conversion from a protein alignment into the corresponding codon alignment can be achieved by replacing each amino acid residue with three nucleotide residues, a procedure which is implemented in several tools, e.g. a”
On the origin and continuing evolution of SARS-CoV-2 (2020, unknown): “31 [40], and the codon alignments were made based on the protein alignment with RevTrans [42].”