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Primary scientific articles also given by this database were discarded.
For this analysis, sequences that were absent either in our 1,025 prokaryotic chromosome dataset or in the ACLAME database were discarded.
Similar(58)
Reads mapped to these two databases were discarded.
The redundant transcripts which overlapped between the two databases were discarded.
Contig hits with e-values larger than 0.01 from homology searches in different reference databases were discarded.
Proteins which showed significant similarity with the databases were discarded and the remaining protein sequences were taken as novel targets.
Then, we used information from AGRIS and plantTFDB to manually screen these putative TFs/TRs, and 223 proteins without supporting information from the two public databases were discarded.
Protein groups matching the reverse database or contaminants were discarded.
Entries that were found as metabolites for a reaction in the KEGG database [ 24] were discarded to restrict our drug list to non-endogenous compounds.
Protein groups with posterior error probability (PEP) values over 0.01 or matches to reversed database or contaminants were discarded.
Of the 435 studies that were identified through database searching, 400 were discarded because they did not meet the criteria (see Table 2).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com