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10.4. Editing Scoring Matrices

The amino scoring matrix files distributed with NCBI-BLAST and WU-BLAST assign a score of +1 to paired stop codons. This doesn't make much biological sense and reduces the ability of TBLASTX to discriminate between coding and noncoding similarities. Therefore, you should edit the scoring matrices to change stop codon pairs to a highly negative score. Be sure to edit the original matrices. The NCBI-BLAST scoring matrices are in the data directory. For WU-BLAST, they are in the matrix/aa directory. The final line of the scoring matrix files looks like this:

* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1 


  

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