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BLAST and phylogenetic analyses of the deduced amino acid sequence indicated that MVCV is a distinct species of the genus Potyvirus and close to Pea seed-borne mosaic virus (PSbMV) with which it forms a new phylogenetic cluster within the genus.
BLASTP analyses of the deduced ORF proteins were performed [ 41].
This phylogenetic tree is further supported by the comparative analyses of the deduced amino acid sequences of the whole DOF proteins by the MEME software.
To further classify the labrid vtgs, we conducted large-scale phylogenetic analyses of the deduced amino acid and codon alignments of available (genbank) and novel genomic (ensembl) variants.
The analyses of the deduced amino acid sequences revealed seven different homologous sequences, with an averaged pairwise distance of 0.38 and a maximum pairwise distance of 0.66.
Our comparative analyses of the deduced amino acid sequences verified that Aegilops section Sitopsis species encode novel HMW-GSs with their molecular weights larger than almost all other known HMW-GSs.
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Our phylogenetic analyses of orthologs deduced from the Plasmodium genomes strongly suggests that the subgenus Laverania was established by a single host switch from birds to African great apes (or vice versa).
d Length (number of amino acids) of the deduced polypeptide.
Phylogenetic analyses of each deduced Mbx protein corroborated the hypothesis that most mbx genes in C. subterraneus subsp. yonseiensis grouped with Thermoanaerobacter species (Additional file 9: Figure S7).
Theoretical analyses of the expansion behavior were deduced from the experimental results.
Note that the cibC gene downstream of cibAB was missed in the annotations and was deduced by analyses of the corresponding nucleotide sequences, based on the nucleotide sequence of S. mitis B6 cibC gene (smi_1957).
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