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

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1 gbasezvalue
2 Function
3
4 Extracts conserved oligomers per position using Z-score
5
6 Description
7
8 This function calculates and extracts conserved oligomers per position using
9 Z-score, in regions around the start/stop codons. The oligomers are returned
10 in ranking order up to "-limit" number.
11
12 The Z-score for mean m and standard error SE is calculated as follows:
13 z = (x - m) / SE
14 where SE for standard deviation s and number of samples s is as follows:
15 SE = s/sqrt(n)
16
17 G-language SOAP service is provided by the
18 Institute for Advanced Biosciences, Keio University.
19 The original web service is located at the following URL:
20
21 http://www.g-language.org/wiki/soap
22
23 WSDL(RPC/Encoded) file is located at:
24
25 http://soap.g-language.org/g-language.wsdl
26
27 Documentation on G-language Genome Analysis Environment methods are
28 provided at the Document Center
29
30 http://ws.g-language.org/gdoc/
31
32 Usage
33
34 Here is a sample session with gbasezvalue
35
36 % gbasezvalue refseqn:NC_000913
37 Extracts conserved oligomers per position using Z-score
38 Program compseq output file (optional) [nc_000913.gbasezvalue]:
39
40 Go to the input files for this example
41 Go to the output files for this example
42
43 Command line arguments
44
45 Standard (Mandatory) qualifiers:
46 [-sequence] seqall Nucleotide sequence(s) filename and optional
47 format, or reference (input USA)
48 [-outfile] outfile [*.gbasezvalue] Program compseq output file
49 (optional)
50
51 Additional (Optional) qualifiers: (none)
52 Advanced (Unprompted) qualifiers:
53 -limit integer [5] Rank threshold for showing the conserved
54 oligomer (Any integer value)
55 -position selection [start] Either 'start' (around start codon)
56 or 'end' (around stop codon) to create the
57 PWM
58 -patlen integer [3] Length of oligomer to count (Any integer
59 value)
60 -upstream integer [30] Length upstream of specified position
61 to create PWM (Any integer value)
62 -downstream integer [30] Length downstream of specified position
63 to create PWM (Any integer value)
64 -[no]accid boolean [Y] Include to use sequence accession ID as
65 query
66
67 Associated qualifiers:
68
69 "-sequence" associated qualifiers
70 -sbegin1 integer Start of each sequence to be used
71 -send1 integer End of each sequence to be used
72 -sreverse1 boolean Reverse (if DNA)
73 -sask1 boolean Ask for begin/end/reverse
74 -snucleotide1 boolean Sequence is nucleotide
75 -sprotein1 boolean Sequence is protein
76 -slower1 boolean Make lower case
77 -supper1 boolean Make upper case
78 -scircular1 boolean Sequence is circular
79 -sformat1 string Input sequence format
80 -iquery1 string Input query fields or ID list
81 -ioffset1 integer Input start position offset
82 -sdbname1 string Database name
83 -sid1 string Entryname
84 -ufo1 string UFO features
85 -fformat1 string Features format
86 -fopenfile1 string Features file name
87
88 "-outfile" associated qualifiers
89 -odirectory2 string Output directory
90
91 General qualifiers:
92 -auto boolean Turn off prompts
93 -stdout boolean Write first file to standard output
94 -filter boolean Read first file from standard input, write
95 first file to standard output
96 -options boolean Prompt for standard and additional values
97 -debug boolean Write debug output to program.dbg
98 -verbose boolean Report some/full command line options
99 -help boolean Report command line options and exit. More
100 information on associated and general
101 qualifiers can be found with -help -verbose
102 -warning boolean Report warnings
103 -error boolean Report errors
104 -fatal boolean Report fatal errors
105 -die boolean Report dying program messages
106 -version boolean Report version number and exit
107
108 Input file format
109
110 The database definitions for following commands are available at
111 http://soap.g-language.org/kbws/embossrc
112
113 gbasezvalue reads one or more nucleotide sequences.
114
115 Output file format
116
117 The output from gbasezvalue is to a plain text file.
118
119 File: nc_000913.gbasezvalue
120
121 Sequence: NC_000913
122 position:-30,1,taa,-0.76525
123 2,aga,-0.79101
124 3,tta,-1.14174
125 4,cta,-1.18831
126 5,aat,-1.86652
127 position:-29,1,cta,-0.18368
128 2,aat,-0.71851
129 3,gac,-1.26182
130 4,taa,-1.39455
131
132 [Part of this file has been deleted for brevity]
133
134 position:29,1,gct,1.66288
135 2,act,1.26637
136 3,tat,0.66721
137 4,cct,-0.43158
138 5,tgt,-0.59254
139 position:30,1,ctg,3.12072
140 2,att,0.04193
141 3,ctc,-0.12416
142 4,cta,-0.38461
143 5,tta,-0.76413
144
145
146 Data files
147
148 None.
149
150 Notes
151
152 None.
153
154 References
155
156 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
157 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
158 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
159
160 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
161 large-scale analysis of high-throughput omics data, J. Pest Sci.,
162 31, 7.
163
164 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
165 Analysis Environment with REST and SOAP Web Service Interfaces,
166 Nucleic Acids Res., 38, W700-W705.
167
168 Warnings
169
170 None.
171
172 Diagnostic Error Messages
173
174 None.
175
176 Exit status
177
178 It always exits with a status of 0.
179
180 Known bugs
181
182 None.
183
184 See also
185
186 gbasecounter Creates a position weight matrix of oligomers around start
187 codon
188 gviewcds Displays a graph of nucleotide contents around start and stop
189 codons
190
191 Author(s)
192
193 Hidetoshi Itaya (celery@g-language.org)
194 Institute for Advanced Biosciences, Keio University
195 252-0882 Japan
196
197 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
198 Institute for Advanced Biosciences, Keio University
199 252-0882 Japan
200
201 History
202
203 2012 - Written by Hidetoshi Itaya
204 2013 - Fixed by Hidetoshi Itaya
205
206 Target users
207
208 This program is intended to be used by everyone and everything, from
209 naive users to embedded scripts.
210
211 Comments
212
213 None.
214