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As expected, a large proportion of sequences (80%, E value cut-off of <10−5) had significant similarities to Phytophthora predicted proteins.
Based on these two experiments, we conclude that the MSA programs tested are capable of accurately aligning the reliable sequences, even in the presence of a large proportion of sequences with discrepancies.
The most represented molecular function was catalytic activity (299 sequences; 49%) and a large proportion of sequences (177; 22%) were associated with membrane as cellular compartment.
In accordance with this, a large proportion of sequences were classified into structural constituent of ribosome and protein-related functions (binding, peptidase activity) regarding molecular function.
In each of the studied viral metagenomes, a large proportion of sequences had no significant homologs identified in Genbank non-redundant database [ 9, 11- 13].
Interestingly, cells cultured under Th17 polarizing conditions were also distinctive, a large proportion of sequences (44%) being Vα11Jα21 (TRAV4D-3 TRaJ27) comprishorta short, 11 amino acid CDR3α loop (AAANTNTGKLT).
Similar(53)
The results are shown in Figure 5; these demonstrate that a large proportion of sequence quartets produced unresolved tree topologies (equivalent to the central portion of the triangle: 19.1%).
The presence of intronic RNAs may influence the sensitivity to detect transcripts, identify splice junctions and measure gene expression levels, as a large proportion of sequence reads is mapped to introns [ 14].
For clusters containing viral homologs, the largest proportion of sequences (59%) were exclusively similar to phage proteins, including those involved in the processes of infection, DNA replication, recombination and repair, DNA modification, nucleotide metablolism, transcripton, translation, lysogeny, synthesis of structural proteins, and cell lysis (Fig. 1B).
Clade 1 contained a larger proportion of sequences from the United States and clade 2 contained a larger proportion of sequences from the European Union for both targets.
The most impacted environments also had the largest proportion of sequences meeting the high similarity threshold.
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