Author: Firth, Andrew E.; Wills, Norma M.; Gesteland, Raymond F.; Atkins, John F.
Title: Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element Document date: 2011_4_27
ID: 2u49b7xo_8
Snippet: Virus sequences were obtained from GenBank in May 2009, updated in October 2010, and processed using BLAST, EMBOSS and ClustalW (52) (53) (54) . The accession numbers of all sequences used are given in the Supplementary Data. Coding sequences were extracted, translated, aligned with ClustalW and back-translated to nucleotide sequence alignments, and manually adjusted in a few cases. For the synonymous site conservation plots, alignment columns in.....
Document: Virus sequences were obtained from GenBank in May 2009, updated in October 2010, and processed using BLAST, EMBOSS and ClustalW (52) (53) (54) . The accession numbers of all sequences used are given in the Supplementary Data. Coding sequences were extracted, translated, aligned with ClustalW and back-translated to nucleotide sequence alignments, and manually adjusted in a few cases. For the synonymous site conservation plots, alignment columns in which the reference sequence ( Figure 4 ) contained gap characters were removed so that the plots are in reference sequence coordinates. RNA structures were predicted using a combination of Vienna RNA RNAfold and alidot, pknotsRG and manual inspection (55, 56) .
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