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date Fri, 26 Jun 2015 05:21:44 -0400
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1 gconsensusz
2 Function
3
4 Calculate consensus in given array of sequences
5
6 Description
7
8 gconsensusz calculates the consensus of given list of sequences, using
9 Z-score. The Z-score will show higher values when the sequences are biased
10 to a single character within the list.
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 gconsensusz
35
36 % gconsensusz consensus.fasta
37 Calculate consensus in given array of sequences
38 Program compseq output file (optional) [rs_000000.gconsensusz]:
39
40 Go to the input files for this example
41 Go to the output files for this example
42
43 Example 2
44
45 % gconsensusz consensus.fasta -plot -graph png
46 Calculate consensus in given array of sequences
47 Created gconsensusz.1.png
48
49 Go to the input files for this example
50 Go to the output files for this example
51
52 Command line arguments
53
54 Standard (Mandatory) qualifiers (* if not always prompted):
55 [-sequence] seqall Nucleotide sequence(s) filename and optional
56 format, or reference (input USA)
57 * -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
58 (ps, hpgl, hp7470, hp7580, meta, cps, x11,
59 tek, tekt, none, data, xterm, png, gif, svg)
60 * -outfile outfile [*.gconsensusz] Program compseq output file
61 (optional)
62
63 Additional (Optional) qualifiers: (none)
64 Advanced (Unprompted) qualifiers:
65 -high integer [1] Z value greater than which is
66 significant (Any integer value)
67 -low float [0.2] Z value less than which is
68 insignificant (Any numeric value)
69 -plot toggle [N] Include to plot result
70
71 Associated qualifiers:
72
73 "-sequence" associated qualifiers
74 -sbegin1 integer Start of each sequence to be used
75 -send1 integer End of each sequence to be used
76 -sreverse1 boolean Reverse (if DNA)
77 -sask1 boolean Ask for begin/end/reverse
78 -snucleotide1 boolean Sequence is nucleotide
79 -sprotein1 boolean Sequence is protein
80 -slower1 boolean Make lower case
81 -supper1 boolean Make upper case
82 -scircular1 boolean Sequence is circular
83 -sformat1 string Input sequence format
84 -iquery1 string Input query fields or ID list
85 -ioffset1 integer Input start position offset
86 -sdbname1 string Database name
87 -sid1 string Entryname
88 -ufo1 string UFO features
89 -fformat1 string Features format
90 -fopenfile1 string Features file name
91
92 "-graph" associated qualifiers
93 -gprompt boolean Graph prompting
94 -gdesc string Graph description
95 -gtitle string Graph title
96 -gsubtitle string Graph subtitle
97 -gxtitle string Graph x axis title
98 -gytitle string Graph y axis title
99 -goutfile string Output file for non interactive displays
100 -gdirectory string Output directory
101
102 "-outfile" associated qualifiers
103 -odirectory string Output directory
104
105 General qualifiers:
106 -auto boolean Turn off prompts
107 -stdout boolean Write first file to standard output
108 -filter boolean Read first file from standard input, write
109 first file to standard output
110 -options boolean Prompt for standard and additional values
111 -debug boolean Write debug output to program.dbg
112 -verbose boolean Report some/full command line options
113 -help boolean Report command line options and exit. More
114 information on associated and general
115 qualifiers can be found with -help -verbose
116 -warning boolean Report warnings
117 -error boolean Report errors
118 -fatal boolean Report fatal errors
119 -die boolean Report dying program messages
120 -version boolean Report version number and exit
121
122 Input file format
123
124 The database definitions for following commands are available at
125 http://soap.g-language.org/kbws/embossrc
126
127 gconsensusz reads one or more nucleotide sequences.
128
129 Output file format
130
131 The output from gconsensusz is to a plain text file or the EMBOSS graphics device.
132
133 File: rs_000000.gconsensusz
134
135 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136
137
138 Data files
139
140 None.
141
142 Notes
143
144 None.
145
146 References
147
148 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
149 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
150 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
151
152 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
153 large-scale analysis of high-throughput omics data, J. Pest Sci.,
154 31, 7.
155
156 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
157 Analysis Environment with REST and SOAP Web Service Interfaces,
158 Nucleic Acids Res., 38, W700-W705.
159
160 Warnings
161
162 None.
163
164 Diagnostic Error Messages
165
166 None.
167
168 Exit status
169
170 It always exits with a status of 0.
171
172 Known bugs
173
174 None.
175
176 See also
177
178 gdistincc Calculates the distance between two loci in circular chromosomes
179 gpalindrome Searches palindrome sequences
180 gseqinfo Prints out basic nucleotide sequence statistics
181
182 Author(s)
183
184 Hidetoshi Itaya (celery@g-language.org)
185 Institute for Advanced Biosciences, Keio University
186 252-0882 Japan
187
188 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
189 Institute for Advanced Biosciences, Keio University
190 252-0882 Japan
191
192 History
193
194 2012 - Written by Hidetoshi Itaya
195 2013 - Fixed by Hidetoshi Itaya
196
197 Target users
198
199 This program is intended to be used by everyone and everything, from
200 naive users to embedded scripts.
201
202 Comments
203
204 None.
205