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

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1 gdeltaenc
2 Function
3
4 Calculate the codon usage bias related to translation optimization
5 (delta ENC)
6
7 Description
8
9 gdeltaenc calculates the codon usage bias related to translation
10 optimization (delta ENC) described in Rocha (2004). The basic idea is to
11 calculate the Effective Number of Codons (ENC) for highly-expressed genes
12 (ribosomal genes) and weakly-expressed genes (all genes), and taking the
13 relative difference between them. ENC assigns a gene a number between 20 to
14 61 where 20 indicates that one codon is used for each aminoacid and 61
15 indicates that each codon is used equally throughout the protein sequence.
16
17 ENC is calculated as follows:
18
19 G-language SOAP service is provided by the
20 Institute for Advanced Biosciences, Keio University.
21 The original web service is located at the following URL:
22
23 http://www.g-language.org/wiki/soap
24
25 WSDL(RPC/Encoded) file is located at:
26
27 http://soap.g-language.org/g-language.wsdl
28
29 Documentation on G-language Genome Analysis Environment methods are
30 provided at the Document Center
31
32 http://ws.g-language.org/gdoc/
33
34 Usage
35
36 Here is a sample session with gdeltaenc
37
38 % gdeltaenc refseqn:NC_000913
39 Calculate the codon usage bias related to translation optimization (delta
40 ENC)
41 Program compseq output file [nc_000913.gdeltaenc]:
42
43 Go to the input files for this example
44 Go to the output files for this example
45
46 Command line arguments
47
48 Standard (Mandatory) qualifiers:
49 [-sequence] seqall Nucleotide sequence(s) filename and optional
50 format, or reference (input USA)
51 [-outfile] outfile [*.gdeltaenc] Program compseq output file
52
53 Additional (Optional) qualifiers: (none)
54 Advanced (Unprompted) qualifiers:
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 gdeltaenc reads one or more nucleotide sequences.
105
106 Output file format
107
108 The output from gdeltaenc is to a plain text file.
109
110 File: nc_000913.gdeltaenc
111
112 Sequence: NC_000913 DELTA-ENC 0.255663430420712
113
114
115 Data files
116
117 None.
118
119 Notes
120
121 None.
122
123 References
124
125 Rocha EPC (2004) Codon usage bias from tRNA's point of view: Redundancy,
126 specialization, and efficient decoding for translation optimization,
127 Genome Research, 14(11):2279-2286
128
129 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
130 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
131 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
132
133 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
134 large-scale analysis of high-throughput omics data, J. Pest Sci.,
135 31, 7.
136
137 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
138 Analysis Environment with REST and SOAP Web Service Interfaces,
139 Nucleic Acids Res., 38, W700-W705.
140
141 Warnings
142
143 None.
144
145 Diagnostic Error Messages
146
147 None.
148
149 Exit status
150
151 It always exits with a status of 0.
152
153 Known bugs
154
155 None.
156
157 See also
158
159 gcbi Calculates the codon bias index (CBI)
160 gicdi Calculates the intrinsic codon deviation index (ICDI)
161 gsvalue Calculate the strength of selected codon usage bias (S)
162
163 Author(s)
164
165 Hidetoshi Itaya (celery@g-language.org)
166 Institute for Advanced Biosciences, Keio University
167 252-0882 Japan
168
169 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
170 Institute for Advanced Biosciences, Keio University
171 252-0882 Japan
172
173 History
174
175 2012 - Written by Hidetoshi Itaya
176 2013 - Fixed by Hidetoshi Itaya
177
178 Target users
179
180 This program is intended to be used by everyone and everything, from
181 naive users to embedded scripts.
182
183 Comments
184
185 None.
186