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comparison GEMBASSY-1.0.3/doc/text/gicdi.txt @ 0:8300eb051bea draft

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1 gicdi
2 Function
3
4 Calculates the intrinsic codon deviation index (ICDI)
5
6 Description
7
8 gicdi calculates the intrinsic codon deviation index (ICDI). ICDI is a
9 measure to estimate codon bias of genes from species in which optimal
10 codons are not known. It is known to show high correlation with other
11 indices such as CBI and ENC. A gene using only one codon for each amino
12 acid will have an ICDI of 1, and a gene using every codon equally for
13 each amino acid will have an ICDI of 0.
14
15 G-language SOAP service is provided by the
16 Institute for Advanced Biosciences, Keio University.
17 The original web service is located at the following URL:
18
19 http://www.g-language.org/wiki/soap
20
21 WSDL(RPC/Encoded) file is located at:
22
23 http://soap.g-language.org/g-language.wsdl
24
25 Documentation on G-language Genome Analysis Environment methods are
26 provided at the Document Center
27
28 http://ws.g-language.org/gdoc/
29
30 Usage
31
32 Here is a sample session with gicdi
33
34 % gicdi refseqn:NC_000913
35 Calculates the intrinsic codon deviation index (ICDI)
36 Codon usage output file [nc_000913.gicdi]:
37
38 Go to the input files for this example
39 Go to the output files for this example
40
41 Command line arguments
42
43 Standard (Mandatory) qualifiers:
44 [-sequence] seqall Nucleotide sequence(s) filename and optional
45 format, or reference (input USA)
46 [-outfile] outfile [*.gicdi] Codon usage output file
47
48 Additional (Optional) qualifiers: (none)
49 Advanced (Unprompted) qualifiers:
50 -translate boolean [N] Include when translating using standard
51 codon table
52 -delkey string [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
53 expression to delete key (Any string)
54 -[no]accid boolean [Y] Include to use sequence accession ID as
55 query
56
57 Associated qualifiers:
58
59 "-sequence" associated qualifiers
60 -sbegin1 integer Start of each sequence to be used
61 -send1 integer End of each sequence to be used
62 -sreverse1 boolean Reverse (if DNA)
63 -sask1 boolean Ask for begin/end/reverse
64 -snucleotide1 boolean Sequence is nucleotide
65 -sprotein1 boolean Sequence is protein
66 -slower1 boolean Make lower case
67 -supper1 boolean Make upper case
68 -scircular1 boolean Sequence is circular
69 -sformat1 string Input sequence format
70 -iquery1 string Input query fields or ID list
71 -ioffset1 integer Input start position offset
72 -sdbname1 string Database name
73 -sid1 string Entryname
74 -ufo1 string UFO features
75 -fformat1 string Features format
76 -fopenfile1 string Features file name
77
78 "-outfile" associated qualifiers
79 -odirectory2 string Output directory
80
81 General qualifiers:
82 -auto boolean Turn off prompts
83 -stdout boolean Write first file to standard output
84 -filter boolean Read first file from standard input, write
85 first file to standard output
86 -options boolean Prompt for standard and additional values
87 -debug boolean Write debug output to program.dbg
88 -verbose boolean Report some/full command line options
89 -help boolean Report command line options and exit. More
90 information on associated and general
91 qualifiers can be found with -help -verbose
92 -warning boolean Report warnings
93 -error boolean Report errors
94 -fatal boolean Report fatal errors
95 -die boolean Report dying program messages
96 -version boolean Report version number and exit
97
98 Input file format
99
100 The database definitions for following commands are available at
101 http://soap.g-language.org/kbws/embossrc
102
103 gicdi reads one or more nucleotide sequences.
104
105 Output file format
106
107 The output from gicdi is to a plain text file.
108
109 File: nc_000913.gicdi
110
111 Sequence: NC_000913
112 icdi,gene
113 0.8192,thrL
114 0.1258,thrA
115 0.1127,thrB
116 0.1689,thrC
117 0.3099,yaaX
118 0.2030,yaaA
119 0.1600,yaaJ
120 0.3533,talB
121
122 [Part of this file has been deleted for brevity]
123
124 0.2203,yjjX
125 0.2719,ytjC
126 0.1377,rob
127 0.2647,creA
128 0.1944,creB
129 0.1733,creC
130 0.1926,creD
131 0.2728,arcA
132 0.5171,yjjY
133 0.2434,yjtD
134
135
136 Data files
137
138 None.
139
140 Notes
141
142 None.
143
144 References
145
146 Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon
147 usage bias, J Mol Evol, 47(3):268-74.
148
149 Freire-Picos MA et al. (1994) Codon usage in Kluyveromyces lactis and in
150 yeast cytochrome c-encoding genes, Gene, 139:43-49.
151
152 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
153 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
154 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
155
156 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
157 large-scale analysis of high-throughput omics data, J. Pest Sci.,
158 31, 7.
159
160 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
161 Analysis Environment with REST and SOAP Web Service Interfaces,
162 Nucleic Acids Res., 38, W700-W705.
163
164 Warnings
165
166 None.
167
168 Diagnostic Error Messages
169
170 None.
171
172 Exit status
173
174 It always exits with a status of 0.
175
176 Known bugs
177
178 None.
179
180 See also
181
182 gcbi Calculates the codon bias index (CBI)
183 gdeltaenc Calculate the codon usage bias related to translation optimization
184 (delta ENC)
185 gsvalue Calculate the strength of selected codon usage bias (S)
186
187 Author(s)
188
189 Hidetoshi Itaya (celery@g-language.org)
190 Institute for Advanced Biosciences, Keio University
191 252-0882 Japan
192
193 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
194 Institute for Advanced Biosciences, Keio University
195 252-0882 Japan
196
197 History
198
199 2012 - Written by Hidetoshi Itaya
200 2013 - Fixed by Hidetoshi Itaya
201
202 Target users
203
204 This program is intended to be used by everyone and everything, from
205 naive users to embedded scripts.
206
207 Comments
208
209 None.
210