MATCH values for BLASTN

Foteos Macrides MACRIDES at wfeb2.bitnet
Wed Sep 11 11:06:00 EST 1991

        The GenBank BLAST Email Server uses defaults of 5 and -4 for parameters
M and N in blastn jobs.  These are described as follows in its HELP file:

     In blastn, M is the score for a single-letter  match;  N  is
     the  score  for  a  single-letter mismatch.  M and N must be
     positive and negative  integers,  respectively.   Given  the
     assumption  made  by  blastn that the 4 nucleotides A, C, G,
     and T are represented equally in the database, the  expected
     score for the query sequence must be negative.

M (but apparently not N) can be changed by providing a value for MATCH in the
job submission file.  What are the considerations and consequences associated
with changes from the default value of 5?


 Foteos Macrides           Worcester Foundation for Experimental Biology
 MACRIDES at WFEB2.BITNET     222 Maple Avenue, Shrewsbury, MA 01545

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