L1ScoringScheme.hh File Reference

class definition for a profile-profile scoring scheme for comparing two sequence profiles using the L1 city-block distance. More...

#include <core/types.hh>
#include <core/sequence/ScoringScheme.hh>

Classes
class	core::sequence::L1ScoringScheme

Namespaces
	core
	A class for reading in the atom type properties.
	core::sequence

Detailed Description

class definition for a profile-profile scoring scheme for comparing two sequence profiles using the L1 city-block distance.

Simply based on comparing single profiles from two protein sequences by computing the sum of P(A) - P(B) for all matching probabilities in the profiles A and B. Also includes with affine gap penalties of the form penalty = A + Bk, where A represents the penalty for starting a gap, and B represents the penalty for extending a previously opened gap by k characters.

Author

James Thompson