Choosing BLAST options for better detection of orthologs as reciprocal best hits

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RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more (2012, methodology): “Orthologs were selected by using a bidirectional best hit method (35), and sequences are masked to eliminate sequence redundancy to assess an”
AnimalTFDB: a comprehensive animal transcription factor database (2011, methodology): “To predict the putative orthologs of these factors among different species, the reciprocal best hit (RBH) method (21) was used.”
Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs (2010, methodology): “Thus, when using BLAST to detect orthologous genes, it could be shown that using the filter only in the seed phase ('soft filtering') increases sensitivity [6].”