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

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1 gscs
2 Function
3
4 Calculates the scaled chi-square
5
6
7 Description
8
9 gscs calculates the Scaled Chi Square (SCS) of each gene. Values of SCS
10 are calculated using completely synonymous codon usage as the expectation
11 and then scaled by dividing the value by the number of codons in the gene
12 excluding Trp and Met.
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 gscs
32
33 % gscs refseqn:NC_000913
34 Calculates the scaled chi-square
35 Codon usage output file [nc_000913.gscs]:
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 [*.gscs] 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 -delkey string [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
52 expression to delete key (i.e. amino acids
53 and nucleotides) (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 gscs reads one or more nucleotide sequences.
104
105 Output file format
106
107 The output from gscs is to a plain text file.
108
109 File: nc_000913.gscs
110
111 Sequence: NC_000913
112 scs,gene
113 1.4458,thrL
114 0.3122,thrA
115 0.2551,thrB
116 0.4104,thrC
117 0.3084,yaaX
118 0.3230,yaaA
119 0.2957,yaaJ
120 0.7101,talB
121
122 [Part of this file has been deleted for brevity]
123
124 0.3054,yjjX
125 0.4076,ytjC
126 0.4231,rob
127 0.3903,creA
128 0.3472,creB
129 0.2695,creC
130 0.3500,creD
131 0.5077,arcA
132 0.4576,yjjY
133 0.2926,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
147 codon usage bias, J Mol Evol, 47(3):268-74.
148
149 Shields DC, Sharp PM. (1987) Synonymous codon usage in Bacillus subtilis
150 reflects both translational selection and mutational biases,
151 15(19):8023-40.
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 genc Calculate the effective number of codons (Nc)
184 gew Calculate a measure of synonymous codon usage evenness (Ew)
185 gfop Calculate the frequency of optimal codons (Fop)
186 gw_value 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