Can somebody tell me what is the "Rank of HSP" in a Blast output? I understand that its the sorted rank, but on what attribute(s) it is sorted? Is it sorted by E-value? I'm using a BLASTX search to find out the Correct Frame for translation of a eukaryotic cDNA sequence, and this is summary of results
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Because of presence of frameshift errors there are multiple hits from different reading frames
Which attribute of hit/HSP would be ideal to choose the frame that most likely contains the coding sequence? Can I choose frame 2 because of HSP_rank 1 corresponds to frame 2?
Thanks
WoA
1 answer
Your output is sorted by e-value, which is the default, though you can produce a tabular blast output and then sort on any attribute you like. I'm not familiar with that style of output and we don't know anything about your target/query sequences, so it's hard to say what to do. If you just want to get ORFs however, I would recommend using a dedicated tool like sixpack or getorf from EMBOSS rather than trying to impute the ORFs from blast hits.
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