Cleaved amplified polymorphic sequence (CAPS) markers.
A CAPS marker is a location a DifferentialCutsite as described below and a set of primers that can be used to visualize this. More information can be found in the paper Konieczny and Ausubel (1993) (PMID 8106085).
- class Bio.CAPS.DifferentialCutsite(**kwds)¶
Differential enzyme cutsite in an alignment.
A differential cutsite is a location in an alignment where an enzyme cuts at least one sequence and also cannot cut at least one other sequence.
start - Where it lives in the alignment.
enzyme - The enzyme that causes this.
cuts_in - A list of sequences (as indexes into the alignment) the enzyme cuts in.
blocked_in - A list of sequences (as indexes into the alignment) the enzyme is blocked in.
- __init__(self, **kwds)¶
Initialize a DifferentialCutsite.
Each member (as listed in the class description) should be included as a keyword.
- exception Bio.CAPS.AlignmentHasDifferentLengthsError¶
Exception where sequences in alignment have different lengths.
- class Bio.CAPS.CAPSMap(alignment, enzymes=None)¶
A map of an alignment showing all possible dcuts.
alignment - The alignment that is mapped.
dcuts - A list of possible CAPS markers in the form of DifferentialCutsites.
- __init__(self, alignment, enzymes=None)¶
Initialize the CAPSMap.
alignment - The alignment to be mapped.
enzymes - List of enzymes to be used to create the map. Defaults to an empty list.