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

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1 gldabias
2 Function
3
4 Calculate strand bias of bacterial genome using linear discriminant
5
6 Description
7
8 gldabias calculates strand bias of bacterial genome using linear
9 discriminant analysis (LDA), as proposed in Reference 1. The basic idea is
10 to use composition data of genes to train and predict the strand of genes
11 residing either on the leading or the lagging strand. For computational
12 efficiency, this method trans and predicts the strands at putative
13 replication origin as reported by the rep_ori_ter() method. This usually
14 results in maximum predictability of LDA within bacterial genomes.
15 Data to use for LDA can be chosen from "base", "codonbase", "codon", and
16 "amino", with -variable option.
17
18 G-language SOAP service is provided by the
19 Institute for Advanced Biosciences, Keio University.
20 The original web service is located at the following URL:
21
22 http://www.g-language.org/wiki/soap
23
24 WSDL(RPC/Encoded) file is located at:
25
26 http://soap.g-language.org/g-language.wsdl
27
28 Documentation on G-language Genome Analysis Environment methods are
29 provided at the Document Center
30
31 http://ws.g-language.org/gdoc/
32
33 Usage
34
35 Here is a sample session with gldabias
36
37 % gldabias refseqn:NC_000913
38 Calculate strand bias of bacterial genome using linear discriminant
39 analysis (LDA)
40 Program compseq output file [nc_000913.gldabias]:
41
42 Go to the input files for this example
43 Go to the output files for this example
44
45 Command line arguments
46
47 Calculate strand bias of bacterial genome using linear discriminant
48 analysis (LDA)
49 Version: EMBOSS:6.5.7.0 GEMBASSY:1.0.1
50
51 Standard (Mandatory) qualifiers:
52 [-sequence] seqall Nucleotide sequence(s) filename and optional
53 format, or reference (input USA)
54 [-outfile] outfile [*.gldabias] Program compseq output file
55
56 Additional (Optional) qualifiers: (none)
57 Advanced (Unprompted) qualifiers:
58 -coefficients integer [0] Show LDA coefficients (Any integer
59 value)
60 -variable selection [codon] Data to use for LDA. Either 'base',
61 'codonbase', 'codon', or 'amino'
62 -[no]accid boolean [Y] Include to use sequence accession ID as
63 query
64
65 Associated qualifiers:
66
67 "-sequence" associated qualifiers
68 -sbegin1 integer Start of each sequence to be used
69 -send1 integer End of each sequence to be used
70 -sreverse1 boolean Reverse (if DNA)
71 -sask1 boolean Ask for begin/end/reverse
72 -snucleotide1 boolean Sequence is nucleotide
73 -sprotein1 boolean Sequence is protein
74 -slower1 boolean Make lower case
75 -supper1 boolean Make upper case
76 -scircular1 boolean Sequence is circular
77 -sformat1 string Input sequence format
78 -iquery1 string Input query fields or ID list
79 -ioffset1 integer Input start position offset
80 -sdbname1 string Database name
81 -sid1 string Entryname
82 -ufo1 string UFO features
83 -fformat1 string Features format
84 -fopenfile1 string Features file name
85
86 "-outfile" associated qualifiers
87 -odirectory2 string Output directory
88
89 General qualifiers:
90 -auto boolean Turn off prompts
91 -stdout boolean Write first file to standard output
92 -filter boolean Read first file from standard input, write
93 first file to standard output
94 -options boolean Prompt for standard and additional values
95 -debug boolean Write debug output to program.dbg
96 -verbose boolean Report some/full command line options
97 -help boolean Report command line options and exit. More
98 information on associated and general
99 qualifiers can be found with -help -verbose
100 -warning boolean Report warnings
101 -error boolean Report errors
102 -fatal boolean Report fatal errors
103 -die boolean Report dying program messages
104 -version boolean Report version number and exit
105
106 Input file format
107
108 The database definitions for following commands are available at
109 http://soap.g-language.org/kbws/embossrc
110
111 gldabias reads one or more nucleotide sequences.
112
113 Output file format
114
115 The output from gldabias is to a plain text file.
116
117 File: nc_000913.gldabias
118
119 Sequence: NC_000913 LDA-BIAS: 0.742533
120
121
122 Data files
123
124 None.
125
126 Notes
127
128 None.
129
130 References
131
132 Rocha EPC et al. (1999) "Universal replication biases in bacteria",
133 Molecular Microbiology, 32(1):11-16
134
135 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
136 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
137 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
138
139 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
140 large-scale analysis of high-throughput omics data, J. Pest Sci.,
141 31, 7.
142
143 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
144 Analysis Environment with REST and SOAP Web Service Interfaces,
145 Nucleic Acids Res., 38, W700-W705.
146
147 Warnings
148
149 None.
150
151 Diagnostic Error Messages
152
153 None.
154
155 Exit status
156
157 It always exits with a status of 0.
158
159 Known bugs
160
161 None.
162
163 See also
164
165 gb1 Calculate strand bias of bacterial genome using B1 index
166 gb2 Calculate strand bias of bacterial genome using B2 index
167 gdeltagcskew Calculate strand bias of bacterial genome using delta GC skew
168 index
169 ggcsi GC Skew Index: an index for strand-specefic mutational bias
170
171 Author(s)
172
173 Hidetoshi Itaya (celery@g-language.org)
174 Institute for Advanced Biosciences, Keio University
175 252-0882 Japan
176
177 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
178 Institute for Advanced Biosciences, Keio University
179 252-0882 Japan
180
181 History
182
183 2012 - Written by Hidetoshi Itaya
184 2013 - Fixed by Hidetoshi Itaya
185
186 Target users
187
188 This program is intended to be used by everyone and everything, from
189 naive users to embedded scripts.
190
191 Comments
192
193 None.
194