The old 'blast -batch' command doesn't work anymore; to run blast in batch mode see How do I run blast searches in batch mode

Why have my alignments changed in Version 9?

Protein sequence alignment programs in the Wisconsin Package use scoring matrices to make comparisons between pairs of amino acids. In Version 9.0, released in December 1996, changes were made to the scoring matrices which may affect the alignments you create. If the sequences you aligned in previous versions of the Package were very similar, you may not have noticed much difference to those same alignments produced using Version 9.0. However, with more distantly related sequences the alignments produced may be substantially different.

Version 9 Changes to Scoring Matrices

There are two main changes to protein scoring matrices in Version 9.0.

• BLOSUM62¹, the new default protein scoring matrix, is the primary cause for the difference in alignments created in Version 9.0. Versions of the Wisconsin Package prior to 9.0 used a scoring matrix based on the PAM250 table from M. Dayhoff², where all perfect matches were set to a single value. BLOSUM62, in contrast, assigns scores ranging from 4 to 11 to perfect matches (identity). Scores for a non-perfect but similar matches range from 0 to 3. Scores for mismatches (non-similar matches) are assigned vales less than 0. Knowing the range of these values is helpful for setting display thresholds for similar amino acids.
• Scoring matrix values are now integers. Matrices which previously held floating point (real number) values have had their values multiplied by 10 so that they now hold integer values. In addition, the values for gap creation and extension penalties also must be entered as integer values.