title: Assessing the significance of a BLASTn score?
body: <p>I am running standalone command line blast to align many query sequences against a large database sequence of nucleotides.  I can modify the command line parameters of the blastn program to change various parameters such as the match/mismatch scores.</p>
  
  <p>I am wondering - for the 'bit score' that blastn outputs, does it make sense to compare the bit scores for alignments with identical query and database sequences but different match/mismatch parameters? I am trying to assess how well blast is performing with various parameter values, but I want to make sure that everything is being compared on even grounds.  Thanks.</p>