#-------------------------  P1HOM/P2HOM (11/ 5/00) --------------------------
item:PXHOM - Dot-matrix similarity (protein)

# The directory fsapdoc must also be available in the $GDE_HELP_DIR,
# containing the file hom.asc from the FSAP package. Again, this
# directory can be implemented as a symbolic link.
itemmethod:readseq -i1 -ffasta -o=in1.seq1 in1; readseq -i2 -ffasta -o=in1.seq2 in1; phom.csh in1.seq1 in1.seq2 in1.out $STARTX $FINISHX $STARTY $FINISHY $RANGE $MINPER $COMPFACT $LINESIZE $PROGRAM; ($GDE_TEXTEDIT in1.out; $RM_CMD in1*) &
itemhelp:doc/fsap/hom.asc
itemopen:gde_help_viewer.csh

arg:STARTX
argtype:slider
arglabel:STARTX
argmin:1
argmax:9000
argvalue:1

arg:FINISHX
argtype:slider
arglabel:FINISHX
argmin:1
argmax:9000
argvalue:9000

arg:STARTY
argtype:slider
arglabel:STARTY
argmin:1
argmax:9000
argvalue:1

arg:FINISHY
argtype:slider
arglabel:FINISHY
argmin:1
argmax:9000
argvalue:9000

arg:PROGRAM
arglabel:K-tuple
argtype:chooser
argchoice:1:p1hom
argchoice:2:p2hom
argvalue:0

arg:RANGE
argtype:slider
arglabel:Dist. from center of window
argmin:1
argmax:30
argvalue:10

arg:MINPER
argtype:slider
arglabel:min. % similarity printed
argmin:5
argmax:100
argvalue:30

arg:COMPFACT
argtype:slider
arglabel:compression factor
argmin:1
argmax:100
argvalue:10

arg:LINESIZE
argtype:slider
arglabel:width (columns) of output line
argmin:40
argmax:150
argvalue:70

in:in1
informat:genbank
insave: