source: tags/initial/GDEHELP/MENUS/blast.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:blastn
2itemmethod:(sed "s/[//%]/>/" <in1 > in1.f; blastn $BLASTDB in1.f W=$WORDLEN M=$MATCH N=$MMSCORE > in1.tmp; ${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1*)&
3itemhelp:blast.help
4
5in:in1
6informat:flat
7insave:
8
9arg:BLASTDB
10argtype:choice_menu
11arglabel:Which Database
12argchoice:genbank:$ARBHOME/GDEHELP/BLAST/genbank
13argchoice:genbank update:$ARBHOME/GDEHELP/BLAST/genupdate
14
15arg:WORDLEN
16argtype:slider
17arglabel:Word Size
18argmin:4
19argmax:18
20argvalue:12
21
22arg:MATCH
23argtype:slider
24arglabel:Match Score
25argmin:1
26argmax:10
27argvalue:5
28
29arg:MMSCORE
30argtype:slider
31arglabel:Mismatch Score
32argmin:-10
33argmax:-1
34argvalue:-5
35
36item:blastx
37itemmethod:(sed "s/[//%]/>/" <in1 > in1.f; cp $ARBHOME/GDEHELP/BLAST/PAM??? .; blastx $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE> in1.tmp; ${ARB_TEXTEDIT:-textedit} in1.tmp; rm in1* PAM???)&
38itemhelp:blast.help
39
40in:in1
41informat:flat
42insave:
43
44arg:BLASTDB
45argtype:choice_menu
46arglabel:Which Database
47argchoice:pir1:$ARBHOME/GDEHELP/BLAST/pir
48argchoice:genpept:$ARBHOME/GDEHELP/BLAST/genpept
49
50arg:WORDLEN
51argtype:slider
52arglabel:Word Size
53argmin:1
54argmax:5
55argvalue:3
56
57arg:Matrix
58arglabel:Substitution Matrix:
59argtype:choice_menu
60argchoice:PAM120:PAM120
61argchoice:PAM250:PAM250
62
63arg:CODE
64argtype:choice_menu
65arglabel:Genetic Code
66argchoice:Standard or Universal:0
67argchoice:Vertebrate Mitochondrial:1
68argchoice:Yeast Mitochondrial:2
69argchoice:Mold Mitochondrial and Mycoplasma:3
70argchoice:Invertebrate Mitochondrial:4
71argchoice:Ciliate Macronuclear:5
72argchoice:Protozoan Mitochondrial:6
73argchoice:Plant Mitochondrial:7
74argchoice:Echinodermate Mitochondrial:8
75
76
77item:FASTA (DNA/RNA)
78itemmethod:(sed "s/[//%]/>/"<in1 >in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; ${ARB_TEXTEDIT:-textedit} in1.out;\rm in1*) &
79itemhelp:FASTA.help
80
81in:in1
82informat:flat
83
84arg:DBASE
85argtype:choice_menu
86arglabel:Database
87argchoice:GenBank Primate:$ARBHOME/GDEHELP/FASTA/GENBANK/gbpri.seq\ 1
88argchoice:GenBank Rodent:$ARBHOME/GDEHELP/FASTA/GENBANK/gbrod.seq\ 1
89argchoice:GenBank all Mammal:$ARBHOME/GDEHELP/FASTA/GENBANK/gbmam.seq\ 1
90argchoice:GenBank verteBrates:$ARBHOME/GDEHELP/FASTA/GENBANK/gbvrt.seq\ 1
91argchoice:GenBank Inverts:$ARBHOME/GDEHELP/FASTA/GENBANK/gbinv.seq\ 1
92argchoice:GenBank pLants:$ARBHOME/GDEHELP/FASTA/GENBANK/gbpln.seq\ 1
93argchoice:GenBank Struct RNA:$ARBHOME/GDEHELP/FASTA/GENBANK/gbrna.seq\ 1
94argchoice:GenBank euk. Organelles:$ARBHOME/GDEHELP/FASTA/GENBANK/gborg.seq\ 1
95argchoice:GenBank phaGe:$ARBHOME/GDEHELP/FASTA/GENBANK/gbphg.seq\ 1
96argchoice:GenBank bacTeria:$ARBHOME/GDEHELP/FASTA/GENBANK/gbbct.seq\ 1
97argchoice:GenBank sYnthetic:$ARBHOME/GDEHELP/FASTA/GENBANK/gbsyn.seq\ 1
98argchoice:GenBank Viral:$ARBHOME/GDEHELP/FASTA/GENBANK/gbvrl.seq\ 1
99argchoice:GenBank Unannotated:$ARBHOME/GDEHELP/FASTA/GENBANK/gbuna.seq\ 1
100
101arg:NUMOFALN
102argtype:slider
103arglabel:Number of Alignment to Report
104argmin:1
105argmax:100
106argvalue:20
107
108arg:MATRIX
109arglabel:Which SMATRIX
110argtype:choice_menu
111argchoice:Default:
112argchoice:altdiag.mat:-s $ARBHOME/GDEHELP/FASTA/MATRIX/altdiag.mat
113argchoice:altprot.mat:-s $ARBHOME/GDEHELP/FASTA/MATRIX/altprot.mat
114argchoice:dna.mat:-s $ARBHOME/GDEHELP/FASTA/MATRIX/dna.mat
115argchoice:prot.mat:-s $ARBHOME/GDEHELP/FASTA/MATRIX/prot.mat
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