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

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1 genc
2 Function
3
4 Calculate the effective number of codons (Nc)
5
6 Description
7
8 genc calculates the effective number of codons (ENC|Nc). ENC is a measure
9 for species-independent codon usage bias. Some measures including CAI are
10 species-dependent as optimal codons differ. ENC assigns a gene a number
11 between 20 to 61 where 20 indicates that one codon is used for each amino
12 acid and 61 indicates that each codon is used equally throughout the
13 protein sequence.
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 genc
33
34 % genc refseqn:NC_000913
35 Calculate the effective number of codons (Nc)
36 Codon usage output file [nc_000913.genc]:
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 [*.genc] Codon usage output file
47
48 Additional (Optional) qualifiers: (none)
49 Advanced (Unprompted) qualifiers:
50 -translate boolean [N] Include when translates using standard
51 codon table
52 -delkey string [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
53 expression to delete key (i.e. amino acids
54 and nucleotides) (Any string)
55 -[no]accid boolean [Y] Include to use sequence accession ID as
56 query
57
58 Associated qualifiers:
59
60 "-sequence" associated qualifiers
61 -sbegin1 integer Start of each sequence to be used
62 -send1 integer End of each sequence to be used
63 -sreverse1 boolean Reverse (if DNA)
64 -sask1 boolean Ask for begin/end/reverse
65 -snucleotide1 boolean Sequence is nucleotide
66 -sprotein1 boolean Sequence is protein
67 -slower1 boolean Make lower case
68 -supper1 boolean Make upper case
69 -scircular1 boolean Sequence is circular
70 -sformat1 string Input sequence format
71 -iquery1 string Input query fields or ID list
72 -ioffset1 integer Input start position offset
73 -sdbname1 string Database name
74 -sid1 string Entryname
75 -ufo1 string UFO features
76 -fformat1 string Features format
77 -fopenfile1 string Features file name
78
79 "-outfile" associated qualifiers
80 -odirectory2 string Output directory
81
82 General qualifiers:
83 -auto boolean Turn off prompts
84 -stdout boolean Write first file to standard output
85 -filter boolean Read first file from standard input, write
86 first file to standard output
87 -options boolean Prompt for standard and additional values
88 -debug boolean Write debug output to program.dbg
89 -verbose boolean Report some/full command line options
90 -help boolean Report command line options and exit. More
91 information on associated and general
92 qualifiers can be found with -help -verbose
93 -warning boolean Report warnings
94 -error boolean Report errors
95 -fatal boolean Report fatal errors
96 -die boolean Report dying program messages
97 -version boolean Report version number and exit
98
99 Input file format
100
101 The database definitions for following commands are available at
102 http://soap.g-language.org/kbws/embossrc
103
104 genc reads one or more nucleotide sequences.
105
106 Output file format
107
108 The output from genc is to a plain text file.
109
110 File: nc_000913.genc
111
112 Sequence: NC_000913
113 enc,gene
114 ,thrL
115 48.41,thrA
116 54.13,thrB
117 46.18,thrC
118 51.65,yaaX
119 45.71,yaaA
120 48.54,yaaJ
121 36.83,talB
122
123 [Part of this file has been deleted for brevity]
124
125 51.43,yjjX
126 46.61,ytjC
127 49.83,rob
128 47.74,creA
129 50.63,creB
130 51.39,creC
131 48.42,creD
132 41.53,arcA
133 61,yjjY
134 53.63,yjtD
135
136
137 Data files
138
139 None.
140
141 Notes
142
143 None.
144
145 References
146
147 Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon
148 usage bias, J Mol Evol, 47(3):268-74.
149
150 Wright F. (1990) The 'effective number of codons' used in a gene, Gene,
151 87:23-29.
152
153 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
154 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
155 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
156
157 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
158 large-scale analysis of high-throughput omics data, J. Pest Sci.,
159 31, 7.
160
161 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
162 Analysis Environment with REST and SOAP Web Service Interfaces,
163 Nucleic Acids Res., 38, W700-W705.
164
165 Warnings
166
167 None.
168
169 Diagnostic Error Messages
170
171 None.
172
173 Exit status
174
175 It always exits with a status of 0.
176
177 Known bugs
178
179 None.
180
181 See also
182
183 gew Calculate a measure of synonymous codon usage evenness (Ew)
184 gfop Calculate the frequency of optimal codons (Fop)
185 gscs Calculates the scaled chi-square
186 gwvalue Calculate the 'relative adaptiveness of each codon' (W)
187
188 Author(s)
189
190 Hidetoshi Itaya (celery@g-language.org)
191 Institute for Advanced Biosciences, Keio University
192 252-0882 Japan
193
194 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
195 Institute for Advanced Biosciences, Keio University
196 252-0882 Japan
197
198 History
199
200 2012 - Written by Hidetoshi Itaya
201 2013 - Fixed by Hidetoshi Itaya
202
203 Target users
204
205 This program is intended to be used by everyone and everything, from
206 naive users to embedded scripts.
207
208 Comments
209
210 None.
211