Pratt
2.1
pattern discovery
K. Sturzrehm, I. Jonassen
pratt
pratt
perl
"pratt"
1
seq
Sequence File
perl
" $value"
4
seqformat
Sequence File format
perl
" $value"
fasta
3
swissprot
fasta
gcg
conservation
Pattern conservation parameters
5
CM
CM: min Nr of Seqs to Match (between 2 and 4)
perl
(defined $value)? " -CM $value":""
5
value must be between 2 and 4
perl
$value && ($value < 2 || $value > 4)
value must be an integer between 2 and 4
perl
$value =~ /\\./
Cpct
C%: min Percentage Seqs to Match
perl
(defined $value && $value != $vdef)? " -C% $value":""
100
5
restrictions
Pattern restrictions parameters
5
PP
PP: pos in seq
perl
($value && $value ne $vdef)? " -PP $value":""
off
5
off
complete
start
you must give a file to define the regions (PF)
perl
$PP && $PP ne "off" && ! $PF
PF
PF: Restriction File name (if PP not off)
perl
" -PF $value"
5
This file contains lines to restrict pattern searches to certain regions in a sequence, say ACE2_YEAST:
>ACE2_YEAST (100,200)
perl
$PP && $PP ne "off"
PL
PL: max Pattern Length
perl
(defined $value && $value != $vdef)? " -PL $value":""
50
5
PN
PN: max Nr of Pattern Symbols
perl
(defined $value && $value != $vdef)? " -PN $value":" -AUTO"
50
5
PX
PX: max Nr of consecutive x's
perl
(defined $value && $value != $vdef)? " -PX $value":""
5
5
FN
FN: max Nr of flexible spacers
perl
(defined $value && $value != $vdef)? " -FN $value":""
2
5
FL
FL: max Flexibility
perl
(defined $value && $value != $vdef)? " -FL $value":""
2
5
FP
FP: max Flex.Product
perl
(defined $value && $value != $vdef)? " -FP $value":""
10
5
BI
BI: Input Pattern Symbol File?
perl
($value)? " -BI on":""
0
5
BF
BF: Input Pattern Symbol File name (if BI on)
perl
($value) ? " -BI $value" : "/local/gensoft/lib/pratt/Pratt.sets.big"
5
default file is: /local/gensoft/lib/pratt/Pratt.sets.big
perl
$BI
BN
BN: Nr of Pattern Symbols Initial Search
perl
(defined $value && $value != $vdef)? " -BN $value":""
20
5
scoring
Pattern Scoring parameters
5
S
S: Scoring
perl
($value && $value != $vdef)? " -S $value":""
info
5
info
mdl
tree
dist
ppv
treefile
Tree File (if Scoring = tree)
perl
" -SF $value "
5
perl
$S eq "tree"
distfile
Distances File (if Scoring = dist)
perl
" -SF $value; "
5
perl
$S eq "dist"
swissprotdb
perl
" -SF /local/gensoft/lib/pratt/sprot.dat"
5
perl
$S eq "ppv"
mdl_param
MDL parameters (Z0-Z3) (if MDL scoring)
perl
$S eq "mdl"
5
Z0
Z0
perl
($value != $vdef)? " -Z0 $value" : ""
10.00
5
perl
$S eq "mdl"
Z1
Z1
perl
($value != $vdef)? " -Z1 $value" : ""
10.00
5
perl
$S eq "mdl"
Z2
Z2
perl
($value != $vdef)? " -Z2 $value" : ""
3.00
5
perl
$S eq "mdl"
Z3
Z3
perl
($value != $vdef)? " -Z3 $value" : ""
10.00
5
perl
$S eq "mdl"
search
Search parameters
5
G
G: Pattern Graph from:
perl
($value && $value ne $vdef)? " -G $value":""
seq
5
seq
al
query
GF
Alignment or Query Filename (if G set to al or query)
perl
" -GF $value"
5
alignment file must be in CLUSTALW format
query file must be in Fasta format
perl
$G eq "al" or $G eq "query"
E
E: Search Greediness
perl
(defined $value && $value != $vdef)? " -E $value":""
3
5
R
R: Pattern Refinement
perl
(! $value)? " -R off" : ""
1
5
RG
RG: Generalise ambiguous symbols (if Pattern Refinement on)
perl
($value)? " -RG on" : ""
0
5
perl
$R
output
Output options
5
OF
OF: Output Filename
perl
($value)? " -OF $value" : ""
5
outfiles
5
*.pat
OP
OP: PROSITE Pattern Format
perl
(! $value)? " -OP off " : ""
1
5
ON
ON: max number patterns
perl
(defined $value && $value != $vdef)? " -ON $value":""
50
5
OA
OA: max number Alignments
perl
(defined $value && $value != $vdef)? " -OA $value":""
50
5
M
M: Print Patterns in sequences
perl
(! $value)? " -M off " : ""
1
5
MR
MR: ratio for printing
perl
(defined $value && $value != $vdef)? " -MR $value":""
10
5
MV
MV: print vertically
perl
($value)? " -MV on " : ""
0
5
report
report