Multiple sequence alignment system and method

A method for aligning characters in character sequences, said method steps comprising:

• identifying a plurality of motifs from said character sequences;
• identifying offending motifs from said plurality of motifs, wherein said offending motifs prevent sequence alignment of the character sequences;
• removing at least one offending motif from consideration at a sequence alignment stage to maximize a pre-specified cost function, wherein the remaining motifs define a feasible set of motifs;
• and
• aligning said character sequences from said feasible set of motifs.

A computer program device readable by a machine, tangibly embodying a program of instructions executable by the machine to perform method steps for aligning characters in character sequences, said method steps comprising:

• identifying a plurality of motifs;
• identifying offending motifs from said plurality of motifs, wherein said offending motifs prevent sequence alignment of the character sequences;
• removing at least one offending motif from consideration at a sequence alignment stage, wherein those motifs not removed from said plurality of motifs define a feasible set of motifs;
• and
• aligning said character sequences from said feasible set of motifs to maximize a pre-specified cost function.