1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
|
infobase
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Return information on a given nucleotide base
Description
infobase reports the defined properties for all known bases, or for any
bases specified by the user.
Usage
Here is a sample session with infobase
% infobase
Return information on a given nucleotide base
Nucleotide base code [ABCDGHKMNRSTUVWXY]:
Output file [outfile.infobase]:
Go to the output files for this example
Command line arguments
Return information on a given nucleotide base
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-code] string [ABCDGHKMNRSTUVWXY] Enter IUPAC nucleotide
base codes, e.g. A, C, G, T, R, Y etc. (Any
string)
[-outfile] outfile [*.infobase] Output file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory2 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
Input file format
infobase uses a string of base codes.
Output file format
infobase outputs a text table of base properties.
Output files for usage example
File: outfile.infobase
Code Ambiguity Complement Mnemonic
A A T adenine
B CGT V not_adenine
C C G cytosine
D AGT H not_cytosine
G G C guanine
H ACT D not_guanine
K GT M keto_base
M AC K amino_base
N ACGT N any_base
R AG Y purine_base
S CG S strong_bond
T T A thymine
U T A uracil
V ACG B not_thymine/uracil
W AT W weak_bond
X ACGT X unknown
Y CT R pyrimidine
Data files
infobase reads the Ebases.iub file to define IUB standard codes for
nucleotides and ambiguity codes.
EMBOSS data files are distributed with the application and stored in
the standard EMBOSS data directory, which is defined by the EMBOSS
environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called ".embossdata". Files
for all EMBOSS runs can be put in the user's home directory, or again
in a subdirectory called ".embossdata".
The directories are searched in the following order:
* . (your current directory)
* .embossdata (under your current directory)
* ~/ (your home directory)
* ~/.embossdata
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None.
See also
Program name Description
inforesidue Return information on a given amino acid residue
Author(s)
Jon Ison
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
History
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
|
