Selected article for: "reference genome and sequence alignment"
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.

    Search related documents:
    Co phrase search for related documents
    • alignment position and genome analysis: 1
    • alignment position and multiple sequence alignment: 1, 2, 3, 4
    • alignment position and pairwise alignment: 1
    • coding region and genome analysis: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22
    • coding region and genome sequence: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
    • coding region and multiple sequence alignment: 1, 2, 3
    • coding region and overlap region: 1, 2
    • coding region and previously describe: 1
    • coding region and reference sequence: 1, 2, 3, 4, 5, 6, 7
    • gap character and multiple sequence alignment: 1
    • gap character and pairwise alignment: 1
    • gap character and reference sequence: 1
    • gap character and reference sequence gap character: 1
    • genome analysis and individual genome sequence: 1
    • genome analysis and multiple sequence alignment: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14
    • genome analysis and previously describe: 1
    • genome analysis and reference sequence: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20
    • genome sequence and previously describe: 1, 2
    • genome sequence and reference sequence: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25