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For each microarray target, the hit with the highest bit score was selected as a match.
Due to length variations between the screened ESTs and the related gene, the retrieved EST with the highest bit score was selected for further analyses.
For each contig (subject) matched by more than one homologue (query), the homologue with the highest alignment bit score was selected.
For each locus, the query sequence that yield the highest bit score was selected as reference to perform homology-based gene prediction using GeneWise (version 2.2.0; [ 72]).
For each region, the query sequence that yields the highest bit score was selected as reference to perform homology-based gene prediction using GeneWise (version 2.2.0; Birney et al. 2004) to avoid fragmented gene models due to unspliced introns.
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First, a pair-wise reciprocal blast was performed of which the best hits based on bit scores were selected.
Specifically, the contigs with the highest bit scores were selected from raw contigs by a homology search against the gene dataset in the TAIR10 database.
Three candidates with the highest score were selected for the next stage.
The associated hits were searched for their respective Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Enzyme Commission Codes (EC) for each query sequence and the highest bit score hit was selected.
The bit score was retained for each TBLASTN sequence alignment.
Additionally, a distinct bit score was required to ensure an unambiguous assignment to one locus.
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