--- doc/psp-gen.xml 2012-06-26 15:38:53.000000000 -0700 +++ /Users/cegrant/projects/meme/doc/psp-gen.xml 2012-06-22 10:23:30.000000000 -0700 @@ -431,13 +431,9 @@ ambiguous characters:
-arbitraryOK
, for
- DNA, N
is recognized as standing for any letter; for
- protein, B
, J
, Z
- and X
are recognized as ambiguous. In either case,
- the effect of encountering any of these letters is to score a word
- or triple containing them as zero (default: ambiguous characters
- cause error termination).
+ The effect of encountering any of these letters is to score a word
+ or triple containing them as if it only occurs once, to minimize its
+ score.
-equiv
option to treat specific groups of letters
@@ -522,7 +518,7 @@
command line reproduces this run:
-time psp-gen -neg pos60k.fasta -pos neg60k.fasta -alpha prot -minw 3 -maxw 50 -arbitraryOK -triples > priors60kmaxw50.psp +time psp-gen -neg pos60k.fasta -pos neg60k.fasta -alpha prot -minw 3 -maxw 50 -triples > priors60kmaxw50.psp
@@ -531,10 +527,10 @@