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

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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