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The A and B alleles at the locus differ by multiple nucleotide and six amino-acid substitutions.
Multiple nucleotide and protein sequence alignments were performed with the ClustalW2 software (www.ebi.ac.uk/Tools/clustalw2/index.html).html
Multiple nucleotide and amino acid variations can be used as input (Fig. 1).
To investigate the phylogenetic relationship of RabV to other WNV isolates, multiple nucleotide and putative amino acid sequence alignments were made involving 16 WNV strains (listed in Table 2).
Phylogenetic analysis was carried out on the multiple nucleotide and amino acid sequence alignments by using maximum parsimony (PAUP* version 4.0b4a Macintosh computer software programs) (28 ) and the distance-based neighbor-joining method.
To examine the cross-species conservation for the CYFIP1 and NIPA2 proteins, the cDNA sequences and their predicted amino acid sequences were compared to multiple nucleotide and protein databases using the BLASTN and BLASTP programs [ 71].
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When sequences of these unique features were compared (megablast and E-value: 1e-4) against 93-11 genome [18], altogether 64883 features showing changes ranging from single to multiple nucleotides and also no matches were identified and were considered together as in-silico predicted −SFP candidates (i.e. Nip>93-11) and rest as non-SFPs (Nip = 93-11).
Metabolic levels were lowered for glycolytic intermediates, a key pentose phosphate pathway intermediate, and multiple nucleotides and intermediates in nucleotide synthesis.
Analyses with multiple nucleotides and analogues [ 36, 37] indicate a distinct regulatory nucleotide-binding site which is most likely to be located in the catalytic domain.
This software is a bioinformatics tool that annotates the variants (SNPs, insertions, deletions, and multiple nucleotide polymorphisms) and calculates the effects they produce on known genes present in the annotation of the reference genome sequence through an algorithm based on interval trees, which is implemented in the Java programming language.
In contrast, the dog and rodent sequences contained multiple nucleotide insertions and /or deletions, resulting in multiple gap insertions throughout the alignment (Figure S1).
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