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The matching pathways from the SMMD are associated with small molecules, each with information about the small molecule concentration, the cell line with which the experiment was conducted and the microarray platform used.
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Only user-selected active pathways from the results table will be queried for matching pathways.
Nucleotide sequences of the predicted proteins from scaffolds were retrieved BEDTools-Version-2.13.1 BEDTools-Version-2.13.1 BEDTools-Version-2.13.1h pathway datasets from curated model species.
To match pathway mentions in text, we employed soft dictionary matching as term variations often cause exact string matching to fail [ 24].
The quality of a candidate model organism is then determined by the degree to which the identified subsystems match genetic pathways from validated knowledge.
cThe number of genes matching KEGG pathways.
Likely due to the low coverage of the wDi proteome, no peptides matching enzymes from Wolbachia pathways for the synthesis of pyrimidines (6 enzymes), lipid II/peptidoglycan (9 enzymes), riboflavin (5 enzymes) or folate (5 enzymes) were detected in any D. immitis tissue.
For each active pathway, we thus search for SMMD records featuring database pathways with a low p-value and with matching genes from the active pathway.
This is in accordance with the intuition that as the divergence of the pair of species increase, any global alignment starts providing more dissimilar mappings, that is, mappings that match reactions from different pathways of the given species.
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Under these criteria, transcripts from more than 7,100 blueberry genes were found to match at least one PlantCyc enzyme sequence, and there were over 450 pathways from PlantCyc that had at least one enzyme matching a blueberry sequence.
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