Author: Anna R. Sjodin; Michael R. Willig; Simon J. Anthony
Title: Quantitative Delineation of Herpesviruses in Bats for use in Ecological Studies Document date: 2019_11_26
ID: 21ldw4lk_12
Snippet: OTU Delineation: A nucleotide alignment of 3,131 herpesvirus clones was conducted using the ClustalW alignment in Geneious version 11.0.5, and a pairwise percent identity (PID) matrix was calculated based on percent similarity of nucleotides in each sequence pair. A PID histogram was then generated (Maes et al. 2009 ). To evaluate the robustness of cutoffs to errors in alignment, the R package Biostrings (Pages et al. 2017 ) was used to conduct p.....
Document: OTU Delineation: A nucleotide alignment of 3,131 herpesvirus clones was conducted using the ClustalW alignment in Geneious version 11.0.5, and a pairwise percent identity (PID) matrix was calculated based on percent similarity of nucleotides in each sequence pair. A PID histogram was then generated (Maes et al. 2009 ). To evaluate the robustness of cutoffs to errors in alignment, the R package Biostrings (Pages et al. 2017 ) was used to conduct pairwise alignments of clones. A second PID histogram was generated, and frequency clusters were compared between the two PIDs. The number of OTUs was estimated using the cutoff extremes for each level of classification, based on total alignment and pairwise alignment (74, 81, 90 and 93 PID cutoffs, see Results and Figure 1 ).
Search related documents:
Co phrase search for related documents, hyperlinks ordered by date