The results that I get after running BLAST+ has many hits, and are always in the same order; no matter how many times I run it for same query against the same database. So what logic is followed to order these hits or is it something that I am missing?
I don't understand? Of course if you run the same query against the same database, the resulting list of hits will be the same - it will not change unless the database itself updates or changes. The hits are ranked by expectation value (E-value, see http://www.ncbi.nlm.nih.gov/blast/tutorial/) which is the number of hits one would expect to see by chance when searching a database of a particular size. The smaller the e-value the more significant is the hit (i.e. the lower the probability of seeing a hit as good purely by chance).
Thanks for the answers.
But what will happen if I have two hits with similar e value?
Then, I think that if the evalue are identical blast order in function of the score. However, you can modify the output of blast in is the parameters.
Best,
Cécile
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