source: tags/initial/GDEHELP/MENUS/blastp.menu

Last change on this file was 2, checked in by oldcode, 24 years ago

Initial revision
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 3.1 KB
Line 
1item:blastp
2itemmethod:(sed "s/[//%]/>/" <in1 > in1.f; cp $ARBHOME/GDEHELP/BLAST/PAM??? .; blastp $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)&
3itemhelp:blast.help
4
5in:in1
6informat:flat
7insave:
8
9arg:BLASTDB
10argtype:choice_menu
11arglabel:Which Database
12argchoice:pir:$ARBHOME/GDEHELP/BLAST/pir
13argchoice:genpept:$ARBHOME/GDEHELP/BLAST/genpept
14argchoice:local:$ARBHOME/GDEHELP/BLAST/local_db
15
16arg:Matrix
17arglabel:Substitution Matrix:
18argtype:choice_menu
19argchoice:PAM120:PAM120
20argchoice:PAM250:PAM250
21
22arg:WORDLEN
23argtype:slider
24arglabel:Word Size
25argmin:1
26argmax:5
27argvalue:3
28
29item:tblastn
30itemmethod:(sed "s/[//%]/>/" <in1 > in1.f; cp $ARBHOME/GDEHELP/BLAST/PAM??? .; tblastn $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE > in1.tmp; ${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)&
31itemhelp:blast.help
32
33in:in1
34informat:flat
35insave:
36
37arg:BLASTDB
38argtype:choice_menu
39arglabel:Which Database
40argchoice:genbank:$ARBHOME/GDEHELP/BLAST/genbank
41argchoice:genbank update:$ARBHOME/GDEHELP/BLAST/genupdate
42
43arg:Matrix
44arglabel:Substitution Matrix:
45argtype:choice_menu
46argchoice:PAM120:PAM120
47argchoice:PAM250:PAM250
48
49arg:WORDLEN
50argtype:slider
51arglabel:Word Size
52argmin:4
53argmax:18
54argvalue:12
55
56arg:CODE
57argtype:choice_menu
58arglabel:Genetic Code
59argchoice:Standard or Universal:0
60argchoice:Vertebrate Mitochondrial:1
61argchoice:Yeast Mitochondrial:2
62argchoice:Mold Mitochondrial and Mycoplasma:3
63argchoice:Invertebrate Mitochondrial:4
64argchoice:Ciliate Macronuclear:5
65argchoice:Protozoan Mitochondrial:6
66argchoice:Plant Mitochondrial:7
67argchoice:Echinodermate Mitochondrial:8
68
69item:blast3
70itemmethod:(sed "s/[//%]/>/" <in1 > in1.f; cp $ARBHOME/GDEHELP/BLAST/PAM??? .; blast3 $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)&
71itemhelp:blast3.help
72
73in:in1
74informat:flat
75insave:
76
77arg:BLASTDB
78argtype:choice_menu
79arglabel:Which Database
80argchoice:pir1:$ARBHOME/GDEHELP/BLAST/pir
81argchoice:genpept:$ARBHOME/GDEHELP/BLAST/genpept
82
83arg:Matrix
84arglabel:Substitution Matrix:
85argtype:choice_menu
86argchoice:PAM120:PAM120
87argchoice:PAM250:PAM250
88
89arg:WORDLEN
90argtype:slider
91arglabel:Word Size
92argmin:1
93argmax:5
94argvalue:3
95
96item:FASTA (Protein)
97itemmethod:(sed "s/[//%]/>/"<in1 >in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; ${ARB_TEXTEDIT:-textedit} in1.out;\rm in1*) &
98itemhelp:FASTA.help
99
100in:in1
101informat:flat
102
103arg:DBASE
104argtype:choice_menu
105arglabel:Database
106argchoice:NBRF PIR1:$ARBHOME/GDEHELP/FASTA/PIR/pir1.dat\ 2
107argchoice:NBRF PIR2:$ARBHOME/GDEHELP/FASTA/PIR/pir2.dat\ 2
108argchoice:NBRF PIR3:$ARBHOME/GDEHELP/FASTA/PIR/pir3.dat\ 2
109
110
111arg:NUMOFALN
112argtype:slider
113arglabel:Number of Alignment to Report
114argmin:1
115argmax:100
116argvalue:20
117
118arg:MATRIX
119arglabel:Which SMATRIX
120argtype:choice_menu
121argchoice:Default:
122argchoice:Minimum mutation matrix:-s $ARBHOME/GDEHELP/FASTA/MATRIX/codaa.mat
123argchoice:Identity matrix:-s $ARBHOME/GDEHELP/FASTA/MATRIX/idnaa.mat
124argchoice:Identity matrix for mismatches:-s $ARBHOME/GDEHELP/FASTA/MATRIX/idpaa.mat
125argchoice:PAM250:-s $ARBHOME/GDEHELP/FASTA/MATRIX/pam250.mat
126argchoice:PAM120:-s $ARBHOME/GDEHELP/FASTA/MATRIX/pam120.mat
127
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