WISE2
2.1.22c
comparisons of protein/DNA sequences
E. Birney
alignment:multiple
wise2
wise2
Wise program
perl
"$value"
1
genewise
estwise
protein
Protein sequence File (if no HMM, see help)
perl
($hmmer) ? " $hmmer" : " $protein"
2
You can either give a protein sequence file or an HMMER file (See HMM Options).
8
You must either give a protein sequence file or an HMMER file
perl
!($hmmer || $protein)
dna
DNA sequence File
perl
" $value"
3
8
quiet
perl
" -silent -quiet"
100
dna_options
DNA sequence Options
5
dna_start
Start position in dna (-u)
perl
(defined $value) ? " -u $value" : ""
5
dna_end
End position in dna (-v)
perl
(defined $value) ? " -v $value" : ""
5
strand
Strand comparison
-tfor
-trev
-both
perl
($value) ? " $value" : ""
5
tabs
Report positions as absolute to truncated/reverse sequence (-tabs)
perl
($value) ? " -tabs" : ""
5
protein_options
Protein comparison Options
perl
! $hmmer
6
protein_start
Start position in protein (-s)
perl
(defined $value) ? " -s $value" : ""
6
perl
! $hmmer
protein_end
End position in protein (-t)
perl
(defined $value) ? " -t $value" : ""
6
perl
! $hmmer
gap
Gap penalty (-g)
perl
(defined $value && $value != $vdef) ? " -g $value" : ""
12
6
perl
! $hmmer
ext
Gap extension penalty (-e)
perl
(defined $value && $value != $vdef) ? " -e $value" : ""
2
6
perl
! $hmmer
HMM_options
HMM Options
7
hmmer
HMMer file (instead of protein) (-hmmer)
perl
($value) ? " -hmmer" : ""
7
hmmfile
perl
$hmmer
hname
Name of HMM rather than using the filename (-hname)
perl
($value) ? " -hname \"$value\"" : ""
7
gene_model_options
Gene Model Options
8
init
Type of match (-init)
perl
($value && $value ne $vdef) ? " -init $value" : ""
default
8
default
global
local
wing
subs
Substitution error rate (-subs)
perl
(defined $value && $value != $vdef) ? " -subs $value" : ""
1e-5
8
indel
Insertion/deletion error rate (-indel)
perl
(defined $value && $value != $vdef) ? " -indel $value" : ""
1e-5
8
cfreq
Using codon bias or not (-cfreq)
perl
($value && $value ne $vdef) ? " -cfreq $value" : ""
flat
8
model
flat
perl
$wise eq "genewise"
splice
Using splice model or GT/AG (-splice)
perl
($value && $value ne $vdef) ? " -splice $value" : ""
model
8
model
flat
perl
$wise2 eq "genewise"
intron
Use tied model for introns (-intron)
perl
($value && $value ne $vdef) ? " -intron $value" : ""
tied
8
model
tied
perl
$wise2 eq "genewise"
null
Random Model as synchronous or flat (-null)
perl
($value && $value ne $vdef) ? " -null $value" : ""
syn
8
syn
flat
alln
Probability of matching a NNN codon (-alln)
perl
($value && $value != $vdef) ? " -alln $value" : ""
1.0
8
insert
Protein insert model (-insert)
perl
($value && $value ne $vdef) ? " -insert $value" : ""
model
flat
flat
8
perl
$wise2 eq "genewise"
output_options
Output Options
10
pretty
Show pretty ascii output (-pretty)
perl
($value) ? " -pretty" : ""
1
10
pseudo
Mark genes with frameshifts as pseudogenes (-pseudo)
perl
($value) ? " -pseudo" : ""
0
10
perl
$wise2 eq "genewise"
genes
Show gene structure (-genes)
perl
($value) ? " -genes" : ""
0
10
perl
$wise2 eq "genewise"
embl
show EMBL feature format with CDS key (-embl)
perl
($value) ? " -embl" : ""
0
10
perl
$wise2 eq "genewise"
diana
show EMBL feature format with misc_feature key for diana (-diana)
perl
($value) ? " -diana" : ""
0
10
perl
$wise2 eq "genewise"
para
Show parameters (-para)
perl
($value) ? " -para" : ""
1
10
sum
Show summary output (-sum)
perl
($value) ? " -sum" : ""
0
10
cdna
Show cDNA (-cdna)
perl
($value) ? " -cdna" : ""
0
10
perl
$wise2 eq "genewise"
trans
Show protein translation (-trans)
perl
($value) ? " -trans" : ""
0
10
perl
$wise2 eq "genewise"
ace
Ace file gene structure (-ace)
perl
($value) ? " -ace" : ""
0
10
perl
$wise2 eq "genewise"
gff
Gene Feature Format file (-gff)
perl
($value) ? " -gff" : ""
0
10
perl
$wise2 eq "genewise"
gener
Raw gene structure (-gener)
perl
($value) ? " -gener" : ""
0
10
perl
$wise2 eq "genewise"
alb
Show logical AlnBlock alignment (-alb)
perl
($value) ? " -alb" : ""
0
10
pal
Show raw matrix alignment (-pal)
perl
($value) ? " -pal" : ""
0
10
block
Length of main block in pretty output (-block)
perl
($value && $value != $vdef) ? " -block $value" : ""
50
10
divide
divide string for multiple outputs (-divide)
perl
($value) ? " -divide \"$value\"" : ""
10
standard_options
Standard Options
11
erroroffstd
No warning messages (-erroroffstd)
perl
($value) ? " -erroroffstd" : ""
0
11