jpayne@69: -- RUNTIME COMPARISON --
jpayne@69: Compute mum candidates of length >= 100.
jpayne@69: Result is identical for both programs.
jpayne@69:  
jpayne@69: 			mummer3:		mummer2:
jpayne@69: 
jpayne@69: Ecoli K12/
jpayne@69: Ecoli 0157: 		14 sec/66 MB		17 sec/133 MB
jpayne@69: 
jpayne@69: Ecoli 0157/
jpayne@69: Ecoli K12: 		14 sec/77 MB		17 sec/155 MB
jpayne@69: 
jpayne@69: S cerevisae/
jpayne@69: S pombe			42 sec/172 MB		50 sec/348 MB
jpayne@69: 
jpayne@69: S pombe/
jpayne@69: S cerevisae		41 sec/176 MB		52 sec/358 MB
jpayne@69: 
jpayne@69: 
jpayne@69: 
jpayne@69: -- CORRECTNESS COMPARISON --
jpayne@69: Consider the two files
jpayne@69: 
jpayne@69: > N25
jpayne@69: NNNNNNNNNNNNNNNNNNNNNNNNN
jpayne@69: 
jpayne@69: and nn.query
jpayne@69: 
jpayne@69: > n18
jpayne@69: nnnnnnnnnnnnnnnnnn
jpayne@69: 
jpayne@69: ------------------ First example:---------------
jpayne@69: mummer3 -l 5 Data/nn.query Data/nn.subject
jpayne@69: > N25
jpayne@69:        1         1        18
jpayne@69:        1         2        18
jpayne@69:        1         3        18
jpayne@69:        1         4        18
jpayne@69:        1         5        18
jpayne@69:        1         6        18
jpayne@69:        1         7        18
jpayne@69:        1         8        18
jpayne@69: 
jpayne@69: mummer2 -l 5 Data/nn.query Data/nn.subject
jpayne@69: > N25
jpayne@69:        1         1        18
jpayne@69: 
jpayne@69: I think the result of mummer3 is correct, since the 
jpayne@69: string n18 occurs exactly once in n18. It occurs 8
jpayne@69: times in N25. hence 8 MUM-candidates are reported.
jpayne@69: 
jpayne@69: ---- second example -----
jpayne@69: 
jpayne@69: mummer3.x -l 5 Data/nn.subject Data/nn.query
jpayne@69: > n18
jpayne@69: 
jpayne@69: Bigmum.sh  -l 5 Data/nn.subject Data/nn.query
jpayne@69: > n18
jpayne@69: New string is suffix of reference string
jpayne@69:        8         1        18
jpayne@69: 
jpayne@69: Here n18 occurs several times in the N25, hence it is 
jpayne@69: not a MUM-candidates and so nothing is to be reported.
jpayne@69: Thus the result of mummer3 is correct.