I have set evalue in BLASTX as 1e-10, I got hits with evalues 2e-39, 3e-40,8e-34. Are these evalues higher/lower than the specified evalue? Should i consider sequences with these new evalues as protein coding?
Evalue of 1e-10 equals to 0.0000000001. This value describes the number of hits you can "expect" to see by chance when searching a database of a particular size. It decreases exponentially as the score of the match increases. For example, an E value of 1 assigned to a hit can be interpreted as meaning that in a database of the current size one might expect to see 1 match with a similar score simply by chance.
Therefore, the lower the E-value, or the closer it is to zero, the more statistically significant the match is. The E-values you have there are very low and thus you should consider these sequences as putative proteins.
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version 2.3.6
What do you think? This should provide a clue.