|
0
|
1 gdinuc
|
|
|
2 Function
|
|
|
3
|
|
|
4 Calculates dinucleotide usage
|
|
|
5
|
|
|
6 Description
|
|
|
7
|
|
|
8 gdinuc calculates dinucleotide usage indices for protein-coding sequences
|
|
|
9 (excluding start and stop codons). Dinucleotide usage is computed as the
|
|
|
10 ratio of observed (O) to expected (E) dinucleotide frequencies within the
|
|
|
11 given sequence. Dinucleotides are known to have consistent patterns within
|
|
|
12 the genome (signatures) and tend to have certain periodicities.
|
|
|
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 gdinuc
|
|
|
32
|
|
|
33 % gdinuc refseqn:NC_000913
|
|
|
34 Calculates dinucleotide usage
|
|
|
35 Program compseq output file [nc_000913.gdinuc]:
|
|
|
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 [*.gdinuc] Program compseq 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 -position menu [all] Codon position or reading frame
|
|
|
52 (Values: all (Assess all codon positions);
|
|
|
53 12 (Assess the reading frame 1-2); 23
|
|
|
54 (Assess the reading frame 2-3); 31 (Assess
|
|
|
55 the reading frame 3-1))
|
|
|
56 -delkey string [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
|
|
|
57 expression to delete key (i.e. amino acids
|
|
|
58 and nucleotides) (Any string)
|
|
|
59 -[no]accid boolean [Y] Include to use sequence accession ID as
|
|
|
60 query
|
|
|
61
|
|
|
62 Associated qualifiers:
|
|
|
63
|
|
|
64 "-sequence" associated qualifiers
|
|
|
65 -sbegin1 integer Start of each sequence to be used
|
|
|
66 -send1 integer End of each sequence to be used
|
|
|
67 -sreverse1 boolean Reverse (if DNA)
|
|
|
68 -sask1 boolean Ask for begin/end/reverse
|
|
|
69 -snucleotide1 boolean Sequence is nucleotide
|
|
|
70 -sprotein1 boolean Sequence is protein
|
|
|
71 -slower1 boolean Make lower case
|
|
|
72 -supper1 boolean Make upper case
|
|
|
73 -scircular1 boolean Sequence is circular
|
|
|
74 -sformat1 string Input sequence format
|
|
|
75 -iquery1 string Input query fields or ID list
|
|
|
76 -ioffset1 integer Input start position offset
|
|
|
77 -sdbname1 string Database name
|
|
|
78 -sid1 string Entryname
|
|
|
79 -ufo1 string UFO features
|
|
|
80 -fformat1 string Features format
|
|
|
81 -fopenfile1 string Features file name
|
|
|
82
|
|
|
83 "-outfile" associated qualifiers
|
|
|
84 -odirectory2 string Output directory
|
|
|
85
|
|
|
86 General qualifiers:
|
|
|
87 -auto boolean Turn off prompts
|
|
|
88 -stdout boolean Write first file to standard output
|
|
|
89 -filter boolean Read first file from standard input, write
|
|
|
90 first file to standard output
|
|
|
91 -options boolean Prompt for standard and additional values
|
|
|
92 -debug boolean Write debug output to program.dbg
|
|
|
93 -verbose boolean Report some/full command line options
|
|
|
94 -help boolean Report command line options and exit. More
|
|
|
95 information on associated and general
|
|
|
96 qualifiers can be found with -help -verbose
|
|
|
97 -warning boolean Report warnings
|
|
|
98 -error boolean Report errors
|
|
|
99 -fatal boolean Report fatal errors
|
|
|
100 -die boolean Report dying program messages
|
|
|
101 -version boolean Report version number and exit
|
|
|
102
|
|
|
103 Input file format
|
|
|
104
|
|
|
105 The database definitions for following commands are available at
|
|
|
106 http://soap.g-language.org/kbws/embossrc
|
|
|
107
|
|
|
108 gdinuc reads one or more nucleotide sequences.
|
|
|
109
|
|
|
110 Output file format
|
|
|
111
|
|
|
112 The output from gdinuc is to a plain text file.
|
|
|
113
|
|
|
114 File: nc_000913.gdinuc
|
|
|
115
|
|
|
116 Sequence: NC_000913
|
|
|
117
|
|
|
118 keys,aa,ac,ag,at,ca,cc,cg,ct,ga,gc,gg,gt,ta,tc,tg,tt,gene,
|
|
|
119 All,1.293,0.921,0.720,1.108,1.022,0.868,1.166,0.925,0.958,1.285,0.897,0.867,0.729,0.891,1.228,1.123,
|
|
|
120
|
|
|
121
|
|
|
122 Data files
|
|
|
123
|
|
|
124 None.
|
|
|
125
|
|
|
126 Notes
|
|
|
127
|
|
|
128 None.
|
|
|
129
|
|
|
130 References
|
|
|
131
|
|
|
132 Yew et al. (2004) Base usage and dinucleotide frequency of infectious
|
|
|
133 bursal disease virus, Virus Genes, 28:1,41-53.
|
|
|
134
|
|
|
135 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
|
|
|
136 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
|
|
|
137 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
|
|
|
138
|
|
|
139 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
|
|
|
140 large-scale analysis of high-throughput omics data, J. Pest Sci.,
|
|
|
141 31, 7.
|
|
|
142
|
|
|
143 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
|
|
|
144 Analysis Environment with REST and SOAP Web Service Interfaces,
|
|
|
145 Nucleic Acids Res., 38, W700-W705.
|
|
|
146
|
|
|
147 Warnings
|
|
|
148
|
|
|
149 None.
|
|
|
150
|
|
|
151 Diagnostic Error Messages
|
|
|
152
|
|
|
153 None.
|
|
|
154
|
|
|
155 Exit status
|
|
|
156
|
|
|
157 It always exits with a status of 0.
|
|
|
158
|
|
|
159 Known bugs
|
|
|
160
|
|
|
161 None.
|
|
|
162
|
|
|
163 See also
|
|
|
164
|
|
|
165 gbui Calculates base usage indices for protein-coding sequences
|
|
|
166
|
|
|
167 Author(s)
|
|
|
168
|
|
|
169 Hidetoshi Itaya (celery@g-language.org)
|
|
|
170 Institute for Advanced Biosciences, Keio University
|
|
|
171 252-0882 Japan
|
|
|
172
|
|
|
173 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
|
|
|
174 Institute for Advanced Biosciences, Keio University
|
|
|
175 252-0882 Japan
|
|
|
176
|
|
|
177 History
|
|
|
178
|
|
|
179 2012 - Written by Hidetoshi Itaya
|
|
|
180 2013 - Fixed by Hidetoshi Itaya
|
|
|
181
|
|
|
182 Target users
|
|
|
183
|
|
|
184 This program is intended to be used by everyone and everything, from
|
|
|
185 naive users to embedded scripts.
|
|
|
186
|
|
|
187 Comments
|
|
|
188
|
|
|
189 None.
|
|
|
190
|
