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Whole nucleotide sequences from these constructs were confirmed by sequencing.
The whole nucleotide sequence of pNH4 was performed and assembled by Phred, Phrap, Consed software [50].
However, the analysed whole nucleotide sets did not show significant saturation effect.
The whole nucleotide sequences of the transposable elements, if possible, were also extracted with the assistance of UniPro uGENE software.
The whole nucleotide sequences of S. cerevisiae, D. melanogaster and P. falciparum were downloaded from the NCBI database (www.ncbi.nlm.nih.gov).nih.gov
Sequences not identified in the alpha and beta group were compared further against nucleic acid coding sequences (delta) and finally the whole nucleotide database (zeta).
Similar(48)
Gepard dotplots of genomes from 24 annotated siphophages that infect E. coli yielded similar relationships whether using whole genome nucleotide or TMP nucleotide sequences.
The following datasets were used: Whole genome nucleotides, all coding genes concatenated nucleotide and amino acid data, each individual gene nucleotide and amino acid data, and the control region nucleotide data.
Representative whole genomes (nucleotide) of adenoviral species 1 56 were selected from the National Center for Biotechnology Information (NCBI), and aligned using the EMBL-EBI Clustal Omega tool61,62.
Phylogenetic relationships were inferred using the maximum likelihood method based upon the Jukes Cantor model for the whole genome nucleotide analysis63, and the Poisson correction model for the fiber-knob amino acid analysis64, using MEGA X software65.
Looking for the MLSA or MLST genes in whole genome nucleotide sequences of the strains under study was realized using of the BLAST v. 2.2.23+ software.
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