Is the score from genewise and exonerate normalized by protein length?

Question

[dukecomeback]

Hi, I want to cutoff the results by scores, but I hope there would be no length bias.

Answer 1

[Jean-Karim Heriche]

From the exonerate documentation:

Alignment Scores
Currently, only the raw alignment scores are displayed. This score just is the sum of transistion scores used in the dynamic programming. For example, in the case of a Smith-Waterman alignment, this will be the sum of the substitution matrix scores and the gap penalties.