Method and system for partitioning sets of sequence groups with respect to a set of subsequence groups, useful for designing polymorphism-based typing assays

A method for partitioning a set of sequence groups into sequence-group partitions with respect to association with a set of subsequences, the individual associations between each sequence in a sequence-group partition and each subsequence in the set of subsequences computable and measurable as a set of values, a sequence-group partition assignable with respect to the set of subsequences when individual associations between the sequences of the sequence-group partition and the set of subsequences are uniquely determined by the measurable set of values, the method comprising:

• creating an empty, sequence-group current partition;
• while the set of sequence groups is not empty,
• attempting to select a candidate group of sequences from the set of sequence groups that can be added to the current sequence-group partition to create a larger sequence-group partition assignable with respect to the set of subsequences,
• when a candidate sequence group is selected, adding the candidate sequence group to the current sequence-group partition and removing the candidate sequence group from the set of sequence groups;
• and
• when a candidate sequence group is not selected, creating a new, empty current sequence-group partition.

A method for partitioning a set of sequence groups into sequence-group partitions with respect to association with a set of subsequence groups, the individual associations between each sequence in a sequence-group partition and each subsequence in a subsequence group computable and measurable as a set of values, a sequence-group partition assignable with respect to a subsequence group when individual associations between the sequences of the sequence-group partition and subsequences of the subsequence group are uniquely determined by the measurable set of values, the method comprising:

• assigning to each sequence group in the set of sequence groups a subsequence group from the set of subsequence groups;
• creating a first empty sequence-group partition;
• considering each sequence group in the set of sequence groups, for each considered sequence group attempting to select a candidate sequence-group partition from among existing sequence-group partitions to which to add the considered sequence group to form a larger sequence-group partitions assignable with respect to the subsequence group associated with the candidate sequence-group partition,
• when a candidate sequence-group partition is selected, adding the considered sequence group to the candidate sequence-group partition, and
• when a candidate sequence-group partition is not selected, creating a new sequence-group partition, adding the considered sequence group to the new sequence-group partition, and associating with the sequence-group partition the subsequence group assigned to the considered sequence group.

A method for partitioning a set of sequence groups into sequence-group partitions with respect to association with a set of subsequence groups, the individual associations between each sequence in a sequence-group partition and each subsequence in a subsequence group computable and measurable as a set of values, a sequence-group partition assignable with respect to a subsequence group when individual associations between the sequences of the sequence-group partition and subsequences of the subsequence group are uniquely determined by the measurable set of values, the method comprising:

• assigning to each sequence-group in the set of groups sequences a subsequence group from the set of subsequence groups;
• creating an empty, current sequence-group partition;
• while the set of sequence groups is not empty,
• attempting to select a candidate sequence group from the set of sequence groups that can be added to the current sequence-group partition to create a larger sequence-group partition assignable with respect to the subsequence group assigned to the current sequence-group partition,
• when a candidate sequence group is selected, adding the candidate sequence group to the current sequence-group partition, removing the candidate sequence group from the set of sequence groups;
• and
• when a candidate group of sequences is not selected, creating a new, empty current sequence-group partition.