Mercurial > repos > ktnyt > gembassy

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial upload
author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:8300eb051bea
1 gdeltagcskew
2 Function
3
4 Calculate strand bias of bacterial genome using delta GC skew index
5
6 Description
7
8 gdeltagcskew calculates strand bias of bacterial genome using delta GC skew
9 index, first proposed by Rocha et al. (2001), and further extended in 2006.
10 Basic idea of delta GC skew index is to calculate the difference of GC skew
11 in coding regions residing in leading and lagging strands. Rocha et al.
12 (2001) calculates delta GC skew index using the third codon position of
13 genes, and Rocha et al. (2006) modified to only use >fourfold degenerate
14 codons.
15
16 G-language SOAP service is provided by the
17 Institute for Advanced Biosciences, Keio University.
18 The original web service is located at the following URL:
19
20 http://www.g-language.org/wiki/soap
21
22 WSDL(RPC/Encoded) file is located at:
23
24 http://soap.g-language.org/g-language.wsdl
25
26 Documentation on G-language Genome Analysis Environment methods are
27 provided at the Document Center
28
29 http://ws.g-language.org/gdoc/
30
31 Usage
32
33 Here is a sample session with gdeltagcskew
34
35 % gdeltagcskew refseqn:NC_000913
36 Calculate strand bias of bacterial genome using delta GC skew index
37 Program compseq output file [nc_000913.gdeltagcskew]:
38
39 Go to the input files for this example
40 Go to the output files for this example
41
42 Command line arguments
43
44 Standard (Mandatory) qualifiers:
45 [-sequence] seqall Nucleotide sequence(s) filename and optional
46 format, or reference (input USA)
47 [-outfile] outfile [*.gdeltagcskew] Program compseq output file
48
49 Additional (Optional) qualifiers: (none)
50 Advanced (Unprompted) qualifiers:
51 -at boolean [N] Include when observing AT skew instead
52 of GC skew
53 -purine boolean [N] Include when observing purine (AG/TC)
54 skew
55 -keto boolean [N] Include when observing keto (TG/AC) skew
56 -method selection [degenerate] Choose the nucleotides to use
57 'degenerate', 'gc3', or 'all'
58 -[no]accid boolean [Y] Include to use sequence accession ID as
59 query
60
61 Associated qualifiers:
62
63 "-sequence" associated qualifiers
64 -sbegin1 integer Start of each sequence to be used
65 -send1 integer End of each sequence to be used
66 -sreverse1 boolean Reverse (if DNA)
67 -sask1 boolean Ask for begin/end/reverse
68 -snucleotide1 boolean Sequence is nucleotide
69 -sprotein1 boolean Sequence is protein
70 -slower1 boolean Make lower case
71 -supper1 boolean Make upper case
72 -scircular1 boolean Sequence is circular
73 -sformat1 string Input sequence format
74 -iquery1 string Input query fields or ID list
75 -ioffset1 integer Input start position offset
76 -sdbname1 string Database name
77 -sid1 string Entryname
78 -ufo1 string UFO features
79 -fformat1 string Features format
80 -fopenfile1 string Features file name
81
82 "-outfile" associated qualifiers
83 -odirectory2 string Output directory
84
85 General qualifiers:
86 -auto boolean Turn off prompts
87 -stdout boolean Write first file to standard output
88 -filter boolean Read first file from standard input, write
89 first file to standard output
90 -options boolean Prompt for standard and additional values
91 -debug boolean Write debug output to program.dbg
92 -verbose boolean Report some/full command line options
93 -help boolean Report command line options and exit. More
94 information on associated and general
95 qualifiers can be found with -help -verbose
96 -warning boolean Report warnings
97 -error boolean Report errors
98 -fatal boolean Report fatal errors
99 -die boolean Report dying program messages
100 -version boolean Report version number and exit
101
102 Input file format
103
104 The database definitions for following commands are available at
105 http://soap.g-language.org/kbws/embossrc
106
107 gdeltagcskew reads one or more nucleotide sequences.
108
109 Output file format
110
111 The output from gdeltagcskew is to a plain text file.
112
113 File: nc_000913.gdeltagcskew
114
115 Sequence: NC_000913 DELTA-GCskew -0.108937
116
117
118 Data files
119
120 None.
121
122 Notes
123
124 None.
125
126 References
127
128 Rocha EPC et al. (2001) Ongoing Evolution of Strand Composition in Bacterial
129 Genomes, Molecular Biology and Evolution, 18(9):1789-1799
130
131 Rocha EPC et al. (2006) Similar compositional biases are caused by very
132 different mutational effects, Genome Research, 16:1537-1547
133
134 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
135 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
136 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
137
138 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
139 large-scale analysis of high-throughput omics data, J. Pest Sci.,
140 31, 7.
141
142 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
143 Analysis Environment with REST and SOAP Web Service Interfaces,
144 Nucleic Acids Res., 38, W700-W705.
145
146 Warnings
147
148 None.
149
150 Diagnostic Error Messages
151
152 None.
153
154 Exit status
155
156 It always exits with a status of 0.
157
158 Known bugs
159
160 None.
161
162 See also
163
164 gb1 Calculate strand bias of bacterial genome using B1 index
165 gb2 Calculate strand bias of bacterial genome using B2 index
166 ggcsi GC Skew Index: an index for strand-specefic mutational bias
167 gldabias Calculate strand bias of bacterial genome using linear
168 discriminant analysis (LDA)
169
170 Author(s)
171
172 Hidetoshi Itaya (celery@g-language.org)
173 Institute for Advanced Biosciences, Keio University
174 252-0882 Japan
175
176 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
177 Institute for Advanced Biosciences, Keio University
178 252-0882 Japan
179
180 History
181
182 2012 - Written by Hidetoshi Itaya
183 2013 - Fixed by Hidetoshi Itaya
184
185 Target users
186
187 This program is intended to be used by everyone and everything, from
188 naive users to embedded scripts.
189
190 Comments
191
192 None.
193