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.
How Does This Affect Me?
Two common questions you may have about the alignments created in Version 9.0 and their answers are detailed below.
Q: The global alignment displayed by PileUp or Gap shows one sequence completely to the right of the others, with only a few end bases shown as matched when run with BLOSUM62 (see examples below). But with the old matrix the sequences appeared to align together. Why?
A: The old matrix (PAM250) was overly permissive of mismatches and allowed you to align unrelated sequences. The BLOSUM62 matrix is more restrictive and will not routinely align unrelated sequences along their entire lengths. Thus, you may find that the displaced sequence(s) may be unrelated to the rest of your alignment. If you have reason to believe that the sequences are globally but very distantly related, then you might want to align them with a matrix based on an evolutionary model that assumes greater divergence time, like BLOSUM30. (A complete series of BLOSUM matrices is provided in the GenMoreData directory.)
(UNIX) prompt> namels genmoredata:blosum*
(OpenVMS) prompt> dir genmoredata:blosom*
51 100 Calm_Human RHVMTNLGEK LTDEEVDEMI READIDGDGQ VNYEEFVQMM TAK~~~~~~~ Calm_Drome RHVMTNLGEK LTDEEVDEMI READIDGDGQ VNYEEFVTMM TSK~~~~~~~ Calm_Wheat RHVMTNLGEK LTDEEVDEMI READVDGDGQ INYEEFVKVM MAK~~~~~~~ Hsp2_Mouse ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~MV RYRMRSPSEG 101 147 Calm_Human ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ Calm_Drome ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ Calm_Wheat ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ Hsp2_Mouse PHQGPGQDHE REEQGQGQGL SPERVEDYGR THRGHHHHRH RRCSRKR |
Global alignments created by PileUp in Version 9.
51 RHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVTMMTSK....... 93 |. : 1 ......................................MVRYRMRSPSEG 12 |