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

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1 gfop
2 Function
3
4 Calculate the frequency of optimal codons (Fop)
5
6 Description
7
8 gfop calculates the frequency of optimal codons (Fop).Fop is an index to
9 show the optimization level of synonymous codon usage choice. It is
10 basically a ratio of optimal codons against all codons used. The value
11 of Fop ranges from 0 (no optimal codons are used) and 1 (only optimal
12 codons are used).
13
14 G-language SOAP service is provided by the
15 Institute for Advanced Biosciences, Keio University.
16 The original web service is located at the following URL:
17
18 http://www.g-language.org/wiki/soap
19
20 WSDL(RPC/Encoded) file is located at:
21
22 http://soap.g-language.org/g-language.wsdl
23
24 Documentation on G-language Genome Analysis Environment methods are
25 provided at the Document Center
26
27 http://ws.g-language.org/gdoc/
28
29 Usage
30
31 Here is a sample session with gfop
32
33 % gfop refseqn:NC_000913
34 Calculate the frequency of optimal codons (Fop)
35 Codon usage output file [nc_000913.gfop]:
36
37 Go to the input files for this example
38 Go to the output files for this example
39
40 Command line arguments
41
42 Standard (Mandatory) qualifiers:
43 [-sequence] seqall Nucleotide sequence(s) filename and optional
44 format, or reference (input USA)
45 [-outfile] outfile [*.gfop] Codon usage output file
46
47 Additional (Optional) qualifiers: (none)
48 Advanced (Unprompted) qualifiers:
49 -translate boolean [N] Include when translates using standard
50 codon table
51 -[no]accid boolean [Y] Include to use sequence accession ID as
52 query
53
54 Associated qualifiers:
55
56 "-sequence" associated qualifiers
57 -sbegin1 integer Start of each sequence to be used
58 -send1 integer End of each sequence to be used
59 -sreverse1 boolean Reverse (if DNA)
60 -sask1 boolean Ask for begin/end/reverse
61 -snucleotide1 boolean Sequence is nucleotide
62 -sprotein1 boolean Sequence is protein
63 -slower1 boolean Make lower case
64 -supper1 boolean Make upper case
65 -scircular1 boolean Sequence is circular
66 -sformat1 string Input sequence format
67 -iquery1 string Input query fields or ID list
68 -ioffset1 integer Input start position offset
69 -sdbname1 string Database name
70 -sid1 string Entryname
71 -ufo1 string UFO features
72 -fformat1 string Features format
73 -fopenfile1 string Features file name
74
75 "-outfile" associated qualifiers
76 -odirectory2 string Output directory
77
78 General qualifiers:
79 -auto boolean Turn off prompts
80 -stdout boolean Write first file to standard output
81 -filter boolean Read first file from standard input, write
82 first file to standard output
83 -options boolean Prompt for standard and additional values
84 -debug boolean Write debug output to program.dbg
85 -verbose boolean Report some/full command line options
86 -help boolean Report command line options and exit. More
87 information on associated and general
88 qualifiers can be found with -help -verbose
89 -warning boolean Report warnings
90 -error boolean Report errors
91 -fatal boolean Report fatal errors
92 -die boolean Report dying program messages
93 -version boolean Report version number and exit
94
95 Input file format
96
97 The database definitions for following commands are available at
98 http://soap.g-language.org/kbws/embossrc
99
100 gfop reads one or more nucleotide sequences.
101
102 Output file format
103
104 The output from gfop is to a plain text file.
105
106 File: nc_000913.gfop
107
108 Sequence: NC_000913
109 Laa,Lc,fop,gene
110 20,5,0.4000,thrL
111 819,133,0.4361,thrA
112 309,46,0.4783,thrB
113 427,69,0.5217,thrC
114 97,7,0.2857,yaaX
115 257,56,0.4643,yaaA
116 475,96,0.3958,yaaJ
117 316,56,0.6964,talB
118
119 [Part of this file has been deleted for brevity]
120
121 169,27,0.2593,yjjX
122 214,23,0.5652,ytjC
123 288,49,0.4082,rob
124 156,23,0.3478,creA
125 228,26,0.3462,creB
126 473,69,0.3478,creC
127 449,70,0.3286,creD
128 237,46,0.6957,arcA
129 45,10,0.7000,yjjY
130 227,24,0.2500,yjtD
131
132
133 Data files
134
135 None.
136
137 Notes
138
139 None.
140
141 References
142
143 Ikemura, T. (1981) Correlation between the abundance of Escherichia coli
144 transfer RNAs and the occurrence of the respective codons in its protein
145 genes: a proposal for a synonymous codon choice that is optimal for the
146 E. coli translational system, J.Mol.Biol, 151:389-409.
147
148 Ikemura (1985) Codon usage and tRNA content in unicellular and multicellular
149 organisms, Mol.Biol.Evol, 2(1):13-34.
150
151 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
152 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
153 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
154
155 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
156 large-scale analysis of high-throughput omics data, J. Pest Sci.,
157 31, 7.
158
159 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
160 Analysis Environment with REST and SOAP Web Service Interfaces,
161 Nucleic Acids Res., 38, W700-W705.
162
163 Warnings
164
165 None.
166
167 Diagnostic Error Messages
168
169 None.
170
171 Exit status
172
173 It always exits with a status of 0.
174
175 Known bugs
176
177 None.
178
179 See also
180
181 genc Calculate the effective number of codons (Nc)
182 gew Calculate a measure of synonymous codon usage evenness (Ew)
183 gscs Calculates the scaled chi-square
184 gwvalue Calculate the 'relative adaptiveness of each codon' (W)
185
186 Author(s)
187
188 Hidetoshi Itaya (celery@g-language.org)
189 Institute for Advanced Biosciences, Keio University
190 252-0882 Japan
191
192 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
193 Institute for Advanced Biosciences, Keio University
194 252-0882 Japan
195
196 History
197
198 2012 - Written by Hidetoshi Itaya
199 2013 - Fixed by Hidetoshi Itaya
200
201 Target users
202
203 This program is intended to be used by everyone and everything, from
204 naive users to embedded scripts.
205
206 Comments
207
208 None.
209