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Old 09-08-2012, 03:56 PM   #3
NormSci
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Location: Canada

Join Date: Apr 2012
Posts: 11
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Hi Tsuyoshi,

After fooling around with blast+ today, I think I've managed to achieve your objective. The command I'm using is:

blastn -query transcripts.fa -out transcripts.blast.txt -task megablast -db refseq_rna -num_threads 12 -evalue 1e-10 -best_hit_score_edge 0.05 -best_hit_overhang 0.25 -outfmt 7 -perc_identity 50 -max_target_seqs 1 &

Adding the "-max_target_seqs" flag and setting it to "1" yields what appears to be the best hit in terms of e-value and bit score. I haven't done extensive comparisons, but it appears where multiple matches yield the same e-value (e.g., 0), the match with the highest score is retained.

Perhaps anyone who has more experience with blast+ can provide further insight.
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