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comparison GEMBASSY-1.0.3/doc/text/gdeltagcskew.txt @ 2:8947fca5f715 draft default tip
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author | ktnyt |
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date | Fri, 26 Jun 2015 05:21:44 -0400 |
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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 |