1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
|
refseqget
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Get reference sequence
Description
refseqget reads a reference sequence and returns the data in one of the
EMBOSS reference sequence formats.
Usage
Here is a sample session with refseqget
% refseqget -of embl
Get reference sequence
-refsequence : enter refseq value: tembl:em498477
Reference sequence output file [em498477.embl]: test.out
Go to the input files for this example
Go to the output files for this example
Command line arguments
Get reference sequence
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-refsequence] refseq (no help text) refseq value
[-outfile] outrefseq (no help text) outrefseq value
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-refsequence" associated qualifiers
-iformat1 string Input reference sequence format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-idbname1 string User-provided database name
"-outfile" associated qualifiers
-odirectory2 string Output directory
-oformat2 string Referece sequence output format
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
Input file format
refseqget reads a reference sequence.
The input is a standard EMBOSS reference sequence query.
The major reference sequence sources are files in one of the common
sequence formats, or remote files accessed by HTTP or FTP.
Input files for usage example
'tembl:em498477' is a sequence entry in the example nucleic acid
database 'tembl'
Database entry: tembl:em498477
ID EM498477; SV 1; linear; genomic DNA; CON; ENV; 1791 BP.
XX
AC EM498477; AACY020000000;
XX
PR Project:PRJNA13694;
XX
DT 14-APR-2007 (Rel. 91, Created)
DT 14-APR-2007 (Rel. 91, Last updated, Version 1)
XX
DE marine metagenome JCVI_SCAF_1096627861213 genomic scaffold, whole genome
DE shotgun sequence.
XX
KW .
XX
OS marine metagenome
OC unclassified sequences; metagenomes; ecological metagenomes.
XX
RN [1]
RP 1-1791
RX DOI; 10.1371/journal.pbio.0050016.
RX PUBMED; 17355171.
RA Yooseph S., Sutton G., Rusch D.B., Halpern A.L., Williamson S.J.,
RA Remington K., Eisen J.A., Heidelberg K.B., Manning G., Li W.,
RA Jaroszewski L., Cieplak P., Miller C.S., Li H., Mashiyama S.T.,
RA Joachimiak M.P., van Belle C., Chandonia J.M., Soergel D.A., Zhai Y.,
RA Natarajan K., Lee S., Raphael B.J., Bafna V., Friedman R., Brenner S.E.,
RA Godzik A., Eisenberg D., Dixon J.E., Taylor S.S., Strausberg R.L.,
RA Frazier M., Venter J.C.;
RT "The Sorcerer II Global Ocean Sampling expedition: expanding the universe
RT of protein families";
RL PLoS Biol. 5(3):e16-e16(2007).
XX
RN [2]
RP 1-1791
RX DOI; 10.1371/journal.pbio.0050017.
RX PUBMED; 17355172.
RA Kannan N., Taylor S.S., Zhai Y., Venter J.C., Manning G.;
RT "Structural and functional diversity of the microbial kinome";
RL PLoS Biol. 5(3):e17-e17(2007).
XX
RN [3]
RP 1-1791
RX DOI; 10.1371/journal.pbio.0050077.
RX PUBMED; 17355176.
RA Rusch D.B., Halpern A.L., Sutton G., Heidelberg K.B., Williamson S.,
RA Yooseph S., Wu D., Eisen J.A., Hoffman J.M., Remington K., Beeson K.,
RA Tran B., Smith H., Baden-Tillson H., Stewart C., Thorpe J., Freeman J.,
RA Andrews-Pfannkoch C., Venter J.E., Li K., Kravitz S., Heidelberg J.F.,
RA Utterback T., Rogers Y.H., Falcon L.I., Souza V., Bonilla-Rosso G.,
RA Eguiarte L.E., Karl D.M., Sathyendranath S., Platt T., Bermingham E.,
RA Gallardo V., Tamayo-Castillo G., Ferrari M.R., Strausberg R.L., Nealson K.,
RA Friedman R., Frazier M., Venter J.C.;
RT "The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic
RT through eastern tropical Pacific";
RL PLoS Biol. 5(3):e77-e77(2007).
XX
RN [4]
RP 1-1791
RG J. Craig Venter Institute
RA ;
RT ;
RL Submitted (02-MAR-2007) to the INSDC.
RL J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850,
RL USA
XX
CC For complete environmental metadata relating to this record,
CC background on the Global Ocean Sampling expedition, as well as
CC additional analysis results, please visit the CAMERA website
CC (http://camera.calit2.net).
XX
FH Key Location/Qualifiers
FH
FT source 1..1791
FT /organism="marine metagenome"
FT /environmental_sample
FT /mol_type="genomic DNA"
FT /isolation_source="isolated as part of a large dataset
FT composed predominantly from surface water marine samples
FT collected along a voyage from Eastern North American coast
FT to the Eastern Pacific Ocean, including locations in the
FT Sargasso Sea, Panama Canal, and the Galapagos Islands"
FT /note="metagenomic"
FT /db_xref="taxon:408172"
XX
CO join(AACY021843949.1:1..897,gap(51),complement(AACY020702065.1:1..843))
//
Output file format
refseqget writes data in one of the reference sequence output formats.
The output is a standard EMBOSS reference sequence.
The major reference sequence formats are the most common sequence
formats.
Output files for usage example
File: test.out
ID EM498477; SV 1; linear; unassigned DNA; STD; UNC; 1791 BP.
XX
DE marine metagenome JCVI_SCAF_1096627861213 genomic scaffold, whole genome
DE shotgun sequence.
XX
SQ Sequence 1791 BP; 583 A; 286 C; 326 G; 545 T; 51 other;
agtacacaat atcctacaaa ttttaatcca ggaacaagtt tctttttggc aaatagtttt 60
gcaagatcac aggcacaatt tttgggagat agcacaggta taacaattaa tgaagttaat 120
agaatatcta aagctactgg accacttact gctgccactg gtgaaacttc atcatcagat 180
ccacatgctg gatttcagct tggtgtatta aatccttatg cttatgaacc tgctgatatt 240
gatgaatgta gtttgttaag cacatgttat tttaaattag gagatgccac ggtagatacg 300
gttaataata caattgatgt tggatttcct catggcctta gtgatttagt tttaggtaga 360
gtttttccgg gggcaggtaa taccttacct actggattaa ctgaaagaaa ttattatata 420
caagttatca attcaacaac acttgcattt tctaccagaa aatcaggaac taccacattt 480
agagcaaatt tatctacttc tggtagtgat gcaggaatag caaaggtttg tattgcaaca 540
gggataacat gttattattt ccaaaccagt ggatatgtat attttaccag ggacactcgc 600
gctcatttta gttataataa taatattgca cgagcacatt tatcgccagt aacaagatgg 660
ggtttacata ctgcaaatac aactgcaagg tctagagttg ataatggatt taattcctta 720
ggaggtgctg atatacgtgc taatcctaat ggattaatgg atataccaga gggtggaaac 780
ggtggcaata atgcacattt atattatcct tatggtagta caagtagaac taataataca 840
aattatttat attatggtat gagattagct cgtactcaag atggtggcac aaattatNNN 900
NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNta tgctagatta 960
ttctgaagat ggtaacgaag atgccgatca gtacgcatta tggcttgcat ataaagaagt 1020
ttccgaaccg aattcgttct acattgcaaa tcatggtttt acaacgggcg acattgtaac 1080
atatagttca actggaactc ttcctgctgg tctcaatggt tttacaacgg caactgctca 1140
aataacaagt gctaacagat ttaaatttaa tagaaatagt gcagcagtaa atattgaaag 1200
tgtaggagtt gctggccaag atattacatt tactgcagtt tcattaaatc cacttggaaa 1260
ttcaattaac ttagtaggaa attcattaac caatggtgaa caagtttcat atacaaataa 1320
tggcgcatca aatattggtg gtcttacaag tggcactagt tattttgttt ttgatagaac 1380
atctgataca attaaacttg ccacaacgtt aactggttat accggagatg aagttttagt 1440
tgatacagat gccacatcag caacaggtgc tgcagcattt attaactcaa caaatggtag 1500
aattcaaggt atttctagta cagcaggaat tgatacgttc caagatggaa gcattgtgca 1560
aatagaacaa gtatccggtt ccactgatca tggattaaaa aatggagcat ttttatttgt 1620
taataaaatt aattccaaaa ccttcgagct ttacccaacc gattctgata gagtggctac 1680
taccaatcaa tatgttccat cacgtacatc agttgatgga caagtaaaat taaaagaaac 1740
cacacttgtt gatttaacag catttgattc tggtacacat agtattacag c 1791
//
Data files
None.
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None.
See also
Program name Description
abiview Display the trace in an ABI sequencer file
coderet Extract CDS, mRNA and translations from feature tables
entret Retrieve sequence entries from flatfile databases and files
extractalign Extract regions from a sequence alignment
infoalign Display basic information about a multiple sequence alignment
infoseq Display basic information about sequences
seqxref Retrieve all database cross-references for a sequence entry
seqxrefget Retrieve all cross-referenced data for a sequence entry
showalign Display a multiple sequence alignment in pretty format
variationget Get sequence variations
whichdb Search all sequence databases for an entry and retrieve it
Author(s)
Peter Rice
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
History
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
|
