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Verification of these connections by ROC analysis suggested that 150 of these genes should be retained as query genes to identify other flowering-time related genes within AraNet because the degree oflowering-time relatedon measured by the ROC AUC increased from 0.1013 (293) to 0.9505 (150).
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High-scoring query genes could then be retained as the new set of query genes.
Only those sequences that detected members of the same family represented by the original query sequence were retained as putative orthologs for those families.
The predicted transcripts that appear both as a query with BLAST hits from one direction and as a subject BLAST hit in the other direction are retained as predicted shared transcripts.
He was retained as painter to George III.
She has been retained as an adviser.
Domenech, surprisingly, was retained as national coach.
Schilling was retained as a consultant.
The best hit for each query sequence is retained, the results of the two (reciprocal) blast are compared, and only the pairs of sequences corresponding to a best hit in both blast are retained as pairs of orthologs.
For those cases where two or more queries matched to overlapping regions of the same protein, all assembled sequences that matched that protein were considered to be possible paralogs and were retained as individual sequences.
The MEROPS batch BLAST [ 91] comparisons were carried out using the putative proteins as the queries, and the MEROPS peptidases as the database, where predicted proteins were queried against all members of the protease database, and sequences with similarity scores (E-value) greater than 1e-04 weretainedned as T. solium protease homologs.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com