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Both the GenBank nucleotide database and the RDP showed multiple instances in which hundreds and even thousands of sequences without taxonomic information appeared as the highest-scoring pairs in BLAST searches, even though there was a named species with 98% identity present in the database.
ASAP also allows description and characterization of the frequent islands of high sequence identity present within the coding regions of sequenced genomes.
However, insights from recent genome projects have shown that nonpathogenic strain of L. biflexa LipL21 protein is an ortholog with ~50% identity present in pathogenic leptospires [ 26].
The latter was obtained by using iterative contig comparison to collate a nonredundant set of distinct contig sequences (<95% sequence identity) present in the set of assemblies, which was annotated using Prokka (Seemann 2014).
We found that the nucleotide sequences between the end of p55 and the right end of the genome were highly variable in the three Xoo phages, with Xp10 and OP1 being more similar to each other than either were to Xop411, and segments with higher degrees of identity present at different positions (see Additional file 4).
Although we only expressed three of the MleiPPs, it is likely that all 10 are functional, considering the very high amino acid identity present within each sequence group and, in particular, the conservation of key functional residues across all Mnemiopsis photoproteins.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com