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

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1 gpalindrome
2 Function
3
4 Searches palindrome sequences
5
6 Description
7
8 gpalindrome searches for palindrome sequences in the genome.
9 Search parameters can be changed for more efficient searches, and g-t
10 matching can be specified by passing the "-gtmatch" qualifier.
11
12 G-language SOAP service is provided by the
13 Institute for Advanced Biosciences, Keio University.
14 The original web service is located at the following URL:
15
16 http://www.g-language.org/wiki/soap
17
18 WSDL(RPC/Encoded) file is located at:
19
20 http://soap.g-language.org/g-language.wsdl
21
22 Documentation on G-language Genome Analysis Environment methods are
23 provided at the Document Center
24
25 http://ws.g-language.org/gdoc/
26
27 Usage
28
29 Here is a sample session with gpalindrome
30
31 % gpalindrome refseqn:NC_000913
32 Searches palindrome sequences
33 Program compseq output file [nc_000913.gpalindrome]:
34
35 Go to the input files for this example
36 Go to the output files for this example
37
38 Command line arguments
39
40 Standard (Mandatory) qualifiers:
41 [-sequence] seqall Nucleotide sequence(s) filename and optional
42 format, or reference (input USA)
43 [-outfile] outfile [*.gpalindrome] Program compseq output file
44
45 Additional (Optional) qualifiers: (none)
46 Advanced (Unprompted) qualifiers:
47 -shortest integer [4] Shortest palindrome to search (Any
48 integer value)
49 -loop integer [0] Longest stem loop to allow (Any integer
50 value)
51 -gtmatch boolean [0] If 1, allows g-t match
52 -[no]accid boolean [Y] Include to use sequence accession ID as
53 query
54
55 Associated qualifiers:
56
57 "-sequence" associated qualifiers
58 -sbegin1 integer Start of each sequence to be used
59 -send1 integer End of each sequence to be used
60 -sreverse1 boolean Reverse (if DNA)
61 -sask1 boolean Ask for begin/end/reverse
62 -snucleotide1 boolean Sequence is nucleotide
63 -sprotein1 boolean Sequence is protein
64 -slower1 boolean Make lower case
65 -supper1 boolean Make upper case
66 -scircular1 boolean Sequence is circular
67 -sformat1 string Input sequence format
68 -iquery1 string Input query fields or ID list
69 -ioffset1 integer Input start position offset
70 -sdbname1 string Database name
71 -sid1 string Entryname
72 -ufo1 string UFO features
73 -fformat1 string Features format
74 -fopenfile1 string Features file name
75
76 "-outfile" associated qualifiers
77 -odirectory2 string Output directory
78
79 General qualifiers:
80 -auto boolean Turn off prompts
81 -stdout boolean Write first file to standard output
82 -filter boolean Read first file from standard input, write
83 first file to standard output
84 -options boolean Prompt for standard and additional values
85 -debug boolean Write debug output to program.dbg
86 -verbose boolean Report some/full command line options
87 -help boolean Report command line options and exit. More
88 information on associated and general
89 qualifiers can be found with -help -verbose
90 -warning boolean Report warnings
91 -error boolean Report errors
92 -fatal boolean Report fatal errors
93 -die boolean Report dying program messages
94 -version boolean Report version number and exit
95
96 Input file format
97
98 The database definitions for following commands are available at
99 http://soap.g-language.org/kbws/embossrc
100
101 gpalindrome reads one or more nucleotide sequences.
102
103 Output file format
104
105 The output from gpalindrome is to a plain text file.
106
107 File: nc_000913.gpalindrome
108
109 Sequence: NC_000913
110 Length, start, end, sequence
111 4,16,18,tg ca
112 4,27,29,at at
113 4,44,46,tt aa
114 4,67,69,ag ct
115 4,97,99,aa tt
116 4,99,101,tt aa
117 10,100,108,taaaa tttta
118 4,132,134,tt aa
119
120 [Part of this file has been deleted for brevity]
121
122 4,4639484,4639486,tg ca
123 6,4639487,4639491,aag ctt
124 4,4639495,4639497,cg cg
125 4,4639506,4639508,ca tg
126 6,4639552,4639556,gtc gac
127 4,4639607,4639609,tg ca
128 4,4639619,4639621,tg ca
129 4,4639621,4639623,ca tg
130 4,4639625,4639627,at at
131 4,4639637,4639639,at at
132
133
134 Data files
135
136 None.
137
138 Notes
139
140 None.
141
142 References
143
144 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
145 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
146 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
147
148 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
149 large-scale analysis of high-throughput omics data, J. Pest Sci.,
150 31, 7.
151
152 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
153 Analysis Environment with REST and SOAP Web Service Interfaces,
154 Nucleic Acids Res., 38, W700-W705.
155
156 Warnings
157
158 None.
159
160 Diagnostic Error Messages
161
162 None.
163
164 Exit status
165
166 It always exits with a status of 0.
167
168 Known bugs
169
170 None.
171
172 See also
173
174 gconsensus_z Calculate consensus in given array of sequences
175 gdist_in_cc Calculates the distance between two loci in circular chromosomes
176 gseqinfo Prints out basic nucleotide sequence statistics
177
178 Author(s)
179
180 Hidetoshi Itaya (celery@g-language.org)
181 Institute for Advanced Biosciences, Keio University
182 252-0882 Japan
183
184 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
185 Institute for Advanced Biosciences, Keio University
186 252-0882 Japan
187
188 History
189
190 2012 - Written by Hidetoshi Itaya
191 2013 - Fixed by Hidetoshi Itaya
192
193 Target users
194
195 This program is intended to be used by everyone and everything, from
196 naive users to embedded scripts.
197
198 Comments
199
200 None.
201