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comparison GEMBASSY-1.0.3/doc/text/gp2.txt @ 0:8300eb051bea draft

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1 gp2
2 Function
3
4 Calculate the P2 index of each gene
5
6 Description
7
8 gp2 calculates the P2 index for each gene. This index describes
9 the proportion of codons conforming to the intermediate strength of
10 codon-anticodon interaction energy rule of Grosjean and Fiers:
11 P2 = (WWC+SSU)/(WWY+SSY) where W = A or U, S = C or G, and Y = C or U.
12 It indicates the efficiency of the codon-anticodon interaction, and has
13 been used as an indicator of the presence of translational selection.
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 gp2
33
34 % gp2 refseqn:NC_000913
35 Calculate the P2 index of each gene
36 Codon usage output file [nc_000913.gp2]:
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 [*.gp2] Codon usage output file
47
48 Additional (Optional) qualifiers: (none)
49 Advanced (Unprompted) qualifiers:
50 -[no]accid boolean [Y] Include to use sequence accession ID as
51 query
52
53 Associated qualifiers:
54
55 "-sequence" associated qualifiers
56 -sbegin1 integer Start of each sequence to be used
57 -send1 integer End of each sequence to be used
58 -sreverse1 boolean Reverse (if DNA)
59 -sask1 boolean Ask for begin/end/reverse
60 -snucleotide1 boolean Sequence is nucleotide
61 -sprotein1 boolean Sequence is protein
62 -slower1 boolean Make lower case
63 -supper1 boolean Make upper case
64 -scircular1 boolean Sequence is circular
65 -sformat1 string Input sequence format
66 -iquery1 string Input query fields or ID list
67 -ioffset1 integer Input start position offset
68 -sdbname1 string Database name
69 -sid1 string Entryname
70 -ufo1 string UFO features
71 -fformat1 string Features format
72 -fopenfile1 string Features file name
73
74 "-outfile" associated qualifiers
75 -odirectory2 string Output directory
76
77 General qualifiers:
78 -auto boolean Turn off prompts
79 -stdout boolean Write first file to standard output
80 -filter boolean Read first file from standard input, write
81 first file to standard output
82 -options boolean Prompt for standard and additional values
83 -debug boolean Write debug output to program.dbg
84 -verbose boolean Report some/full command line options
85 -help boolean Report command line options and exit. More
86 information on associated and general
87 qualifiers can be found with -help -verbose
88 -warning boolean Report warnings
89 -error boolean Report errors
90 -fatal boolean Report fatal errors
91 -die boolean Report dying program messages
92 -version boolean Report version number and exit
93
94 Input file format
95
96 The database definitions for following commands are available at
97 http://soap.g-language.org/kbws/embossrc
98
99 gp2 reads one or more nucleotide sequences.
100
101 Output file format
102
103 The output from gp2 is to a plain text file.
104
105 File: nc_000913.gp2
106
107 Sequence: NC_000913
108 P2,gene
109 0.4444,thrL
110 0.4234,thrA
111 0.4565,thrB
112 0.5156,thrC
113 0.4074,yaaX
114 0.4494,yaaA
115 0.3621,yaaJ
116 0.6832,talB
117
118 [Part of this file has been deleted for brevity]
119
120 0.3692,yjjX
121 0.4912,ytjC
122 0.4271,rob
123 0.4318,creA
124 0.3065,creB
125 0.3851,creC
126 0.4320,creD
127 0.6395,arcA
128 0.7857,yjjY
129 0.3333,yjtD
130
131
132 Data files
133
134 None.
135
136 Notes
137
138 None.
139
140 References
141
142 Gouy M, Gautier C. (1982) Codon usage in bacteria: correlation with gene
143 expressivity, Nucleic Acids Res, 10(22):7055-74.
144
145 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
146 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
147 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
148
149 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
150 large-scale analysis of high-throughput omics data, J. Pest Sci.,
151 31, 7.
152
153 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
154 Analysis Environment with REST and SOAP Web Service Interfaces,
155 Nucleic Acids Res., 38, W700-W705.
156
157 Warnings
158
159 None.
160
161 Diagnostic Error Messages
162
163 None.
164
165 Exit status
166
167 It always exits with a status of 0.
168
169 Known bugs
170
171 None.
172
173 See also
174
175 gcai Calculate codon adaptation index for each gene
176 gphx Identify predicted highly expressed gene
177
178 Author(s)
179
180 Hidetoshi Itaya (celery@g-language.org)
181 Institute for Advanced Biosciences, Keio University
182 252-0882 Japan
183
184 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
185 Institute for Advanced Biosciences, Keio University
186 252-0882 Japan
187
188 History
189
190 2012 - Written by Hidetoshi Itaya
191 2013 - Fixed by Hidetoshi Itaya
192
193 Target users
194
195 This program is intended to be used by everyone and everything, from
196 naive users to embedded scripts.
197
198 Comments
199
200 None.
201