Extra Exercises Attempt to use the wonderful looking Cinema with your PAX6 sequences. A profile is a table that contains all of the comparison information of a group of aligned sequences. It contains as many rows as there are positions in the aligned sequences. Each row contains a score for the alignment of the corresponding position of the aligned sequences with each possible residue. Match values are higher at conserved positions.
Care needs to be taken that the profile is balanced.
HMMs can be used to do multiple sequence alignment and database searching, using statistical descriptions of a sequence family's consensus. We expect that over the next few years, programs will increasingly use these rather than table profiles. The major problem with profiles is the computational time required. Create the Profile Select the pax6.msf file from the main list . Select profilemake from the Multiple Comparison menu Now run this.