Author: Valeria Lulla; Andrew E. Firth
Title: A hidden gene in astroviruses encodes a cell-permeabilizing protein involved in virus release Document date: 2019_6_6
ID: avq3zwmc_38
Snippet: Synonymous site conservation was analyzed with SYNPLOT2 9 . For the full-genome analyses we generated codon-respecting alignments using a procedure described previously 9 . In brief, each individual genome sequence was aligned to a reference sequence using code2aln version 1.2 32 . Genomes were then mapped to reference sequence coordinates by removing alignment positions that contained a gap character in the reference sequence, and these pairwise.....
Document: Synonymous site conservation was analyzed with SYNPLOT2 9 . For the full-genome analyses we generated codon-respecting alignments using a procedure described previously 9 . In brief, each individual genome sequence was aligned to a reference sequence using code2aln version 1.2 32 . Genomes were then mapped to reference sequence coordinates by removing alignment positions that contained a gap character in the reference sequence, and these pairwise alignments were combined to give the multiple sequence alignment. To assess conservation at synonymous sites, the ORF1a, ORF1b and ORF2 coding regions were extracted from the alignment (with codons selected from the longer ORF in each overlap region), concatenated inframe, and the alignment analyzed with SYNPLOT2 using a 25-codon sliding window.
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