Selected article for: "database sequence and generate sequence"
Author: Mathew, Suneeth F.; Crowe-McAuliffe, Caillan; Graves, Ryan; Cardno, Tony S.; McKinney, Cushla; Poole, Elizabeth S.; Tate, Warren P.
Title: The Highly Conserved Codon following the Slippery Sequence Supports -1 Frameshift Efficiency at the HIV-1 Frameshift Site
  • Document date: 2015_3_25
    • ID: 10p3mth2_7
    Snippet: HIV-1 sequences were downloaded from the Los Alamos National Laboratory (http://www. hiv.lanl.gov/) sequence database and aligned with MAFFT (v. 6.903b) [36] . Only sequences that encoded an intact, aligned slippery sequence (TTTTTTA) and that passed quality control checks used by the Los Alamos National Laboratory (i.e. were free of additional frameshift mutations, premature stop codons, and apparent hypermutation) were analysed. Sequences with .....
    Document: HIV-1 sequences were downloaded from the Los Alamos National Laboratory (http://www. hiv.lanl.gov/) sequence database and aligned with MAFFT (v. 6.903b) [36] . Only sequences that encoded an intact, aligned slippery sequence (TTTTTTA) and that passed quality control checks used by the Los Alamos National Laboratory (i.e. were free of additional frameshift mutations, premature stop codons, and apparent hypermutation) were analysed. Sequences with ambiguous base calls in the intercodon were excluded. In total, 3534 of 4675 total sequences met these criteria and were used for further analysis. The BioPython (v. 1.59) toolset was used for further sequence analysis [37] . WebLogo (v. 2.8.2) was used to generate sequence logos [38] .

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