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

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1 goligomersearch
2 Function
3
4 Searches oligomers in given sequence
5
6 Description
7
8 goligomersearch searches for the given oligomer in given sequence. Oligomer
9 can be specified using degenerate nucleotide alphabet, or by regular
10 expressions. Performance is optimized for fast searching.
11 This method changes the returning value according to the given options.
12
13 G-language SOAP service is provided by the
14 Institute for Advanced Biosciences, Keio University.
15 The original web service is located at the following URL:
16
17 http://www.g-language.org/wiki/soap
18
19 WSDL(RPC/Encoded) file is located at:
20
21 http://soap.g-language.org/g-language.wsdl
22
23 Documentation on G-language Genome Analysis Environment methods are
24 provided at the Document Center
25
26 http://ws.g-language.org/gdoc/
27
28 Usage
29
30 Here is a sample session with goligomersearch
31
32 % goligomersearch refseqn:NC_000913 atgcatgc
33 Searches oligomers in given sequence
34 Program compseq output file [nc_000913.goligomersearch]:
35
36 Go to the input files for this example
37 Go to the output files for this example
38
39 Command line arguments
40
41 Standard (Mandatory) qualifiers:
42 [-sequence] seqall Nucleotide sequence(s) filename and optional
43 format, or reference (input USA)
44 [-oligomer] string Oligomer to search (Any string)
45 [-outfile] outfile [*.goligomersearch] Program compseq output
46 file
47
48 Additional (Optional) qualifiers: (none)
49 Advanced (Unprompted) qualifiers:
50 -return selection [position] 'position' to return list of
51 positions where oligomers are found, 'oligo'
52 to return list of oligomers found ordered
53 by positions, 'both' to return a hash with
54 positions as keys and oligomers as values,
55 'distribution' to return four values about
56 the distribution of given oligomer
57 -[no]accid boolean [Y] Include to use sequence accession ID as
58 query
59
60 Associated qualifiers:
61
62 "-sequence" associated qualifiers
63 -sbegin1 integer Start of each sequence to be used
64 -send1 integer End of each sequence to be used
65 -sreverse1 boolean Reverse (if DNA)
66 -sask1 boolean Ask for begin/end/reverse
67 -snucleotide1 boolean Sequence is nucleotide
68 -sprotein1 boolean Sequence is protein
69 -slower1 boolean Make lower case
70 -supper1 boolean Make upper case
71 -scircular1 boolean Sequence is circular
72 -sformat1 string Input sequence format
73 -iquery1 string Input query fields or ID list
74 -ioffset1 integer Input start position offset
75 -sdbname1 string Database name
76 -sid1 string Entryname
77 -ufo1 string UFO features
78 -fformat1 string Features format
79 -fopenfile1 string Features file name
80
81 "-outfile" associated qualifiers
82 -odirectory3 string Output directory
83
84 General qualifiers:
85 -auto boolean Turn off prompts
86 -stdout boolean Write first file to standard output
87 -filter boolean Read first file from standard input, write
88 first file to standard output
89 -options boolean Prompt for standard and additional values
90 -debug boolean Write debug output to program.dbg
91 -verbose boolean Report some/full command line options
92 -help boolean Report command line options and exit. More
93 information on associated and general
94 qualifiers can be found with -help -verbose
95 -warning boolean Report warnings
96 -error boolean Report errors
97 -fatal boolean Report fatal errors
98 -die boolean Report dying program messages
99 -version boolean Report version number and exit
100
101 Input file format
102
103 The database definitions for following commands are available at
104 http://soap.g-language.org/kbws/embossrc
105
106 goligomersearch reads one or more nucleotide sequences.
107
108 Output file format
109
110 The output from goligomersearch is to a plain text file.
111
112 File: nc_000913.goligomersearch
113
114 Sequence: NC_000913 Oligomer: atgcatgc Return: 147018,366819,653138,863326,1288615,1627117,2111200,2246695,2697278,2750962,2826906,2882353,2998362,3022134,3346029,3477018,3629113,3842819,3958304,3982183,4013480,4285578,4474663,4484501,4499080,4604562,4638391
115
116
117 Data files
118
119 None.
120
121 Notes
122
123 None.
124
125 References
126
127 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
128 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
129 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
130
131 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
132 large-scale analysis of high-throughput omics data, J. Pest Sci.,
133 31, 7.
134
135 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
136 Analysis Environment with REST and SOAP Web Service Interfaces,
137 Nucleic Acids Res., 38, W700-W705.
138
139 Warnings
140
141 None.
142
143 Diagnostic Error Messages
144
145 None.
146
147 Exit status
148
149 It always exits with a status of 0.
150
151 Known bugs
152
153 None.
154
155 See also
156
157 gkmertable Create an image showing all k-mer abundance within a
158 sequence
159 gnucleotideperiodicity Checks the periodicity of certain oligonucleotides
160 goligomercounter Counts the number of given oligomers in a sequence
161 gsignature Calculate oligonucleotide usage (genomic signature)
162
163 Author(s)
164
165 Hidetoshi Itaya (celery@g-language.org)
166 Institute for Advanced Biosciences, Keio University
167 252-0882 Japan
168
169 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
170 Institute for Advanced Biosciences, Keio University
171 252-0882 Japan
172
173 History
174
175 2012 - Written by Hidetoshi Itaya
176 2013 - Fixed by Hidetoshi Itaya
177
178 Target users
179
180 This program is intended to be used by everyone and everything, from
181 naive users to embedded scripts.
182
183 Comments
184
185 None.
186