|
0
|
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
|
