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1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
2 "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
3 <html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en' lang='en'>
4 <head>
5 <title>EMBOSS: genret manual</title>
6 <link rel='stylesheet' type='text/css' href='/gembassy/emboss_explorer/style/emboss.css' />
7
8 </head>
9 <body>
10 <div id='manual'>
11 <!-- tfm output starts here -->
12
13
14
15
16 <table align=center border=0 cellspacing=0 cellpadding=0>
17 <tr><td valign=top>
18 <A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a>
19 </td>
20 <td align=left valign=middle>
21 <b><font size="+6">
22 genret
23 </font></b>
24 </td></tr>
25 </table>
26 <br>&nbsp;
27 <p>
28
29
30 <!--END OF HEADER-->
31
32
33
34
35
36
37 <H2> Function </H2>
38 Retrieves various gene related information from genome flatfile
39 <!--
40 DON'T WRITE ANYTHING HERE.
41 IT IS DONE FOR YOU.
42 -->
43
44
45
46
47 <H2>Description</H2>
48 <p>
49 genret reads in one or more genome flatfiles and retrieves various data from<br />
50 the input file. It is a wrapper program to the G-language REST service,<br />
51 where a method is specified by giving a string to the "method" qualifier. By<br />
52 default, genret will parse the input file to retrieve the accession ID<br />
53 (or name) of the genome to query G-language REST service. By setting the<br />
54 "accid" qualifier to false (or 0), genret will instead parse the sequence<br />
55 and features of the genome to create a GenBank formatted flatfile and upload<br />
56 the file to the G-language web server. Using the file uploaded, genret will<br />
57 execute the method provided.<br />
58 <br />
59 genret is able to perform a variety of tasks, incluing the retrieval of<br />
60 sequence upstream, downstream, or around the start or stop codon,<br />
61 translated gene sequences search of gene data by keyword.<br />
62 <br />
63 Details on G-language REST service is available from the wiki page<br />
64 <br />
65 http://www.g-language.org/wiki/rest<br />
66 <br />
67 Documentation on G-language Genome Analysis Environment methods are<br />
68 provided at the Document Center<br />
69 <br />
70 http://ws.g-language.org/gdoc/<br />
71 <br />
72
73 </p>
74
75 <H2>Usage</H2>
76
77 Here is a sample session with genret<br><br>
78
79 Retrieving sequences upstream, downstream, or around the start/stop codons.
80 The following example shows the retrieval of sequence around the start
81 codons of all genes.<br><br>
82
83 Genes to access are specified by regular expression. '*' stands for every
84 gene.<br><br>
85
86 Available methods are:<br>
87 after_startcodon<br>
88 after_stopcodon<br>
89 around_startcodon<br>
90 around_stopcodon<br>
91 before_startcodon<br>
92 before_stopcodon<br><br>
93
94 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
95
96 % genret
97 Retrieves various gene related information from genome flatfile
98 Input nucleotide sequence(s): refseqn:NC_000913
99 Gene name(s) to lookup [*]:
100 Feature to access: around_startcodon
101 Full text output file [nc_000913.around_startcodon]:
102
103 </pre></td></tr></table>
104
105 Go to the <a href="#input">input files</a> for this example<br>
106 Go to the <a href="#output">output files</a> for this example<br><br>
107
108 Example 2<br><br>
109
110 Using flat text as target genes. The names can be split with with a space, comma, or vertical bar.<br><br>
111
112 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
113
114 % genret
115 Retrieves various gene related information from genome flatfile
116 Input nucleotide sequence(s): refseqn:NC_000913
117 List of gene name(s) to report [*]: recA,recB
118 Name of gene feature to access: translation
119 Sequence output file [nc_000913.translation.genret]: stdout
120 >recA
121 MAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGR
122 IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDT
123 GEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNL
124 KQSNTLLIFINQIRMKIGVMFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSETR
125 VKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKAN
126 ATAWLKDNPETAKEIEKKVRELLLSNPNSTPDFSVDDSEGVAETNEDF
127 >recB
128 MSDVAETLDPLRLPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLV
129 VTFTEAATAELRGRIRSNIHELRIACLRETTDNPLYERLLEEIDDKAQAAQWLLLAERQMD
130 EAAVFTIHGFCQRMLNLNAFESGMLFEQQLIEDESLLRYQACADFWRRHCYPLPREIAQVV
131 FETWKGPQALLRDINRYLQGEAPVIKAPPPDDETLASRHAQIVARIDTVKQQWRDAVGELD
132 ALIESSGIDRRKFNRSNQAKWIDKISAWAEEETNSYQLPESLEKFSQRFLEDRTKAGGETP
133 RHPLFEAIDQLLAEPLSIRDLVITRALAEIRETVAREKRRRGELGFDDMLSRLDSALRSES
134 GEVLAAAIRTRFPVAMIDEFQDTDPQQYRIFRRIWHHQPETALLLIGDPKQAIYAFRGADI
135 FTYMKARSEVHAHYTLDTNWRSAPGMVNSVNKLFSQTDDAFMFREIPFIPVKSAGKNQALR
136 FVFKGETQPAMKMWLMEGESCGVGDYQSTMAQVCAAQIRDWLQAGQRGEALLMNGDDARPV
137 RASDISVLVRSRQEAAQVRDALTLLEIPSVYLSNRDSVFETLEAQEMLWLLQAVMTPEREN
138 TLRSALATSMMGLNALDIETLNNDEHAWDVVVEEFDGYRQIWRKRGVMPMLRALMSARNIA
139 ENLLATAGGERRLTDILHISELLQEAGTQLESEHALVRWLSQHILEPDSNASSQQMRLESD
140 KHLVQIVTIHKSKGLEYPLVWLPFITNFRVQEQAFYHDRHSFEAVLDLNAAPESVDLAEAE
141 RLAEDLRLLYVALTRSVWHCSLGVAPLVRRRGDKKGDTDVHQSALGRLLQKGEPQDAAGLR
142 TCIEALCDDDIAWQTAQTGDNQPWQVNDVSTAELNAKTLQRLPGDNWRVTSYSGLQQRGHG
143 IAQDLMPRLDVDAAGVASVVEEPTLTPHQFPRGASPGTFLHSLFEDLDFTQPVDPNWVREK
144 LELGGFESQWEPVLTEWITAVLQAPLNETGVSLSQLSARNKQVEMEFYLPISEPLIASQLD
145 TLIRQFDPLSAGCPPLEFMQVRGMLKGFIDLVFRHEGRYYLLDYKSNWLGEDSSAYTQQAM
146 AAAMQAHRYDLQYQLYTLALHRYLRHRIADYDYEHHFGGVIYLFLRGVDKEHPQQGIYTTR
147 PNAGLIALMDEMFAGMTLEEA
148
149 </pre></td></tr></table>
150
151 Go to the <a href="#input">input files</a> for this example<br>
152 Go to the <a href="#output">output files</a> for this example<br><br>
153
154 Example 3<br><br>
155
156 Using a file with a list of gene names.
157 The following example will retrieve the strand direction for each gene
158 listed in the "gene_list.txt" file. String prefixed with an "@" or "list::"
159 will be interpreted as file names.<br><br>
160
161 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
162
163 % genret
164 Retrieves various gene features from genome flatfile
165 Input nucleotide sequence(s): refseqn:NC_000913
166 List of gene name(s) to report [*]: @gene_list.txt
167 Name of gene feature to access: direction
168 Full text output file [nc_000913.direction]: stdout
169 gene,direction
170 thrA,direct
171 thrB,direct
172 thrC,direct
173
174 </pre></td></tr></table>
175
176 Example 4<br><br>
177
178 Retrieving translations of coding sequences.<br>
179 The following example will retrieve the translated protein sequence of
180 the "recA" gene.<br><br>
181
182 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
183
184 % genret
185 Retrieves various gene related information from genome flatfile
186 Input nucleotide sequence(s): refseqn:NC_000913
187 Gene name(s) to lookup [*]: recA
188 Feature to access: translation
189 Full text output file [nc_000913.translation]: stdout
190 >recA
191 MAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGR
192 IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDT
193 GEQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNL
194 KQSNTLLIFINQIRMKIGVMFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSETR
195 VKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKAN
196 ATAWLKDNPETAKEIEKKVRELLLSNPNSTPDFSVDDSEGVAETNEDF
197
198 </pre></td></tr></table>
199
200 Go to the <a href="#input">input files</a> for this example<br>
201 Go to the <a href="#output">output files</a> for this example<br><br>
202
203 Example 5<br><br>
204
205 Retrieving feature information of the genes.<br>
206 The following example will retrieve the start positions for each gene.
207 The values for the keys in GenBank format is available for retrieval.
208 (ex. start end direction GO* etc.)<br>
209 Positions will be returned with a 1 start value.<br><br>
210
211 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
212
213 % genret
214 Retrieves various gene related information from genome flatfile
215 Input nucleotide sequence(s): refseqn:NC_000913
216 Gene name(s) to lookup [*]:
217 Feature to access: start
218 Full text output file [nc_000913.start]:
219
220 </pre></td></tr></table>
221
222 Go to the <a href="#input">input files</a> for this example<br>
223 Go to the <a href="#output">output files</a> for this example<br><br>
224
225 Example 6<br><br>
226
227 Passing extra arguments to the methods.<br>
228 The following example shows the retrieval of 30 base pairs around the
229 start codon of the "recA" gene. By default, the "around_startcodon" method
230 returns 200 base pairs around the start codon. Using the "-argument"
231 qualifier allows the user to change this value.<br><br>
232
233 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
234
235 % genret refseqn:NC_000913 recA around_startcodon -argument 30,30 stdout
236 Retrieves various gene features from genome flatfile
237 >recA
238 ccggtattacccggcatgacaggagtaaaaatggctatcgacgaaaacaaacagaaagcgt
239 tg
240
241 </pre></td></tr></table>
242
243 Go to the <a href="#input">input files</a> for this example<br>
244 Go to the <a href="#output">output files</a> for this example<br><br>
245
246 Example 7<br><br>
247
248 Re-annotating a flatfile.
249 genret supports re-annotation of a genome flatfile via Restauro-G
250 service developed by our team.
251 The original software is available at [<a href="http://restauro-g.iab.keio.ac.jp/">http://restauro-g.iab.keio.ac.jp</a>].<br><br>
252
253 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
254
255 % genret refseqn:NC_000913 '*' annotate nc_000913-annotate.gbk
256 Retrieves various gene features from genome flatfile
257
258 </pre></td></tr></table>
259
260 Go to the <a href="#input">input files</a> for this example<br>
261 Go to the <a href="#output">output files</a> for this example<br><br>
262
263 <h2>Command line arguments</h2>
264
265 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
266 <tr bgcolor="#FFFFCC">
267 <th align="left">Qualifier</th>
268 <th align="left">Type</th>
269 <th align="left">Description</th>
270 <th align="left">Allowed values</th>
271 <th align="left">Default</th>
272 </tr>
273
274 <tr bgcolor="#FFFFCC">
275 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
276 </tr>
277
278 <tr bgcolor="#FFFFCC">
279 <td>[-sequence]<br>(Parameter 1)</td>
280 <td>seqall</td>
281 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
282 <td>Readable sequence(s)</td>
283 <td><b>Required</b></td>
284 </tr>
285
286 <tr bgcolor="#FFFFCC">
287 <td>[-gene]<br>(Parameter 2)</td>
288 <td>string</td>
289 <td>List of gene name(s) to report</td>
290 <td>Any string</td>
291 <td>*</td>
292 </tr>
293
294 <tr bgcolor="#FFFFCC">
295 <td>[-access]<br>(Parameter 3)</td>
296 <td>string</td>
297 <td>Name of gene feature to access</td>
298 <td>Any word</td>
299 <td>&nbsp;</td>
300 </tr>
301
302 <tr bgcolor="#FFFFCC">
303 <td>[-outfile]<br>(Parameter 4)</td>
304 <td>outfile</td>
305 <td>Sequence output file</td>
306 <td>Output file</td>
307 <td><i>&lt;*&gt;</i>.genret</td>
308 </tr>
309
310 <tr bgcolor="#FFFFCC">
311 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
312 </tr>
313
314 <tr>
315 <td colspan=5>(none)</td>
316 </tr>
317
318 <tr bgcolor="#FFFFCC">
319 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
320 </tr>
321
322 <tr bgcolor="#FFFFCC">
323 <td>-argument</td>
324 <td>string</td>
325 <td>Extra arguments to pass to method</td>
326 <td>Any string</td>
327 <td>&nbsp;</td>
328 </tr>
329
330 <tr bgcolor="#FFFFCC">
331 <td>-[no]accid</td>
332 <td>boolean</td>
333 <td>Include to use sequence accession ID as query</td>
334 <td>Boolean value Yes/No</td>
335 <td>Yes</td>
336 </tr>
337
338 </table>
339
340
341 <h2 id="input">Input file format</h2>
342
343 <p>
344 Database definitions for the examples are included in the embossrc_template<br />
345 file of the Keio Bioinformatcs Web Service (KBWS) package.<br />
346 <br />
347 Input files for usage example 4<br />
348 <br />
349 File: gene_list.txt<br />
350 <br />
351 thrA<br />
352 thrB<br />
353 thrC<br />
354 <br />
355
356 </p>
357
358 <h2 id="output">Output file format</h2>
359
360 <p>
361 Output files for usage example 1<br />
362 <br />
363 File: nc_000913.around_startcodon<br />
364 <br />
365 <table width="90%"><tr><td bgcolor="#CCFFCC">
366 >thrL<br />
367 cgtgagtaaattaaaattttattgacttaggtcactaaatactttaaccaatataggcata<br />
368 gcgcacagacagataaaaattacagagtacacaacatccatgaaacgcattagcaccacca<br />
369 ttaccaccaccatcaccattaccacaggtaacggtgcgggctgacgcgtacaggaaacaca<br />
370 gaaaaaagcccgcacctgac<br />
371 >thrA<br />
372 aggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtgc<br />
373 gggctttttttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcggcg<br />
374 gtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgc<br />
375 caggcaggggcaggtggcca<br />
376 <br />
377 <font color=red>[Part of this file has been deleted for brevity]</font><br />
378 <br />
379 >yjjY<br />
380 tgcatgtttgctacctaaattgccaactaaatcgaaacaggaagtacaaaagtccctgacc<br />
381 tgcctgatgcatgctgcaaattaacatgatcggcgtaacatgactaaagtacgtaattgcg<br />
382 ttcttgatgcactttccatcaacgtcaacaacatcattagcttggtcgtgggtactttccc<br />
383 tcaggacccgacagtgtcaa<br />
384 >yjtD<br />
385 tttttctgcgacttacgttaagaatttgtaaattcgcaccgcgtaataagttgacagtgat<br />
386 cacccggttcgcggttatttgatcaagaagagtggcaatatgcgtataacgattattctgg<br />
387 tcgcacccgccagagcagaaaatattggggcagcggcgcgggcaatgaaaacgatggggtt<br />
388 tagcgatctgcggattgtcg<br />
389 </td></tr></table>
390 <br />
391 Output files for usage example 3<br />
392 <br />
393 File: nc_000913.start<br />
394 <br />
395 <table width="90%"><tr><td bgcolor="#CCFFCC">
396 gene,start<br />
397 thrL,190<br />
398 thrA,337<br />
399 thrB,2801<br />
400 thrC,3734<br />
401 yaaX,5234<br />
402 yaaA,5683<br />
403 yaaJ,6529<br />
404 talB,8238<br />
405 mog,9306<br />
406 <br />
407 <font color=red>[Part of this file has been deleted for brevity]</font><br />
408 <br />
409 yjjX,4631256<br />
410 ytjC,4631820<br />
411 rob,4632464<br />
412 creA,4633544<br />
413 creB,4634030<br />
414 creC,4634719<br />
415 creD,4636201<br />
416 arcA,4637613<br />
417 yjjY,4638425<br />
418 yjtD,4638965<br />
419 </td></tr></table><br />
420
421 Output files for usage example 7<br />
422 <br />
423 File: ecoli-annotate.gbk<br />
424 <br />
425 <table width="90%"><tr><td bgcolor="#CCFFCC">
426 LOCUS NC_000913 4639675 bp DNA circular BCT 25-OCT-2010<br />
427 DEFINITION Escherichia coli str. K-12 substr. MG1655 chromosome, complete<br />
428 genome.<br />
429 ACCESSION NC_000913<br />
430 VERSION NC_000913.2 GI:49175990<br />
431 DBLINK Project: 57779<br />
432 KEYWORDS .<br />
433 SOURCE Escherichia coli str. K-12 substr. MG1655<br />
434 ORGANISM Escherichia coli str. K-12 substr. MG1655<br />
435 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;<br />
436 <br />
437 <font color="red">[Part of this file has been deleted for brevity]</font><br />
438 <br />
439 CDS 2801..3733<br />
440 /EC_number="2.7.1.39"<br />
441 /codon_start="1"<br />
442 /db_xref="GI:16127997"<br />
443 /db_xref="ASAP:ABE-0000010"<br />
444 /db_xref="UniProtKB/Swiss-Prot:P00547"<br />
445 /db_xref="ECOCYC:EG10999"<br />
446 /db_xref="EcoGene:EG10999"<br />
447 /db_xref="GeneID:947498"<br />
448 /function="enzyme; Amino acid biosynthesis: Threonine"<br />
449 /function="1.5.1.8 metabolism; building block<br />
450 biosynthesis; amino acids; threonine"<br />
451 /function="7.1 location of gene products; cytoplasm"<br />
452 /gene="thrB"<br />
453 /gene_synonym="ECK0003; JW0002"<br />
454 /locus_tag="b0003"<br />
455 /note="GO_component: GO:0005737 - cytoplasm; GO_process:<br />
456 GO:0009088 - threonine biosynthetic process"<br />
457 /product="homoserine kinase"<br />
458 /protein_id="NP_414544.1"<br />
459 /rs_com="FUNCTION: Catalyzes the ATP-dependent<br />
460 phosphorylation of L- homoserine to L-homoserine<br />
461 phosphate (By similarity)."<br />
462 /rs_com="CATALYTIC ACTIVITY: ATP + L-homoserine = ADP +<br />
463 O-phospho-L- homoserine."<br />
464 /rs_com="PATHWAY: Amino-acid biosynthesis; L-threonine<br />
465 biosynthesis; L- threonine from L-aspartate: step 4/5."<br />
466 /rs_com="SUBCELLULAR LOCATION: Cytoplasm (Potential)."<br />
467 /rs_com="SIMILARITY: Belongs to the GHMP kinase family.<br />
468 Homoserine kinase subfamily."<br />
469 /rs_des="RecName: Full=Homoserine kinase; Short=HK;<br />
470 Short=HSK; EC=2.7.1.39;"<br />
471 /rs_protein="Level 1: similar to KHSE_ECODH 1.7e-180"<br />
472 /rs_xr="EMBL; CP000948; ACB01208.1; -; Genomic_DNA."<br />
473 /rs_xr="RefSeq; YP_001728986.1; -."<br />
474 /rs_xr="ProteinModelPortal; B1XBC8; -."<br />
475 /rs_xr="SMR; B1XBC8; 2-308."<br />
476 /rs_xr="EnsemblBacteria; EBESCT00000012034;<br />
477 EBESCP00000011562; EBESCG00000011096."<br />
478 /rs_xr="GeneID; 6058639; -."<br />
479 /rs_xr="GenomeReviews; CP000948_GR; ECDH10B_0003."<br />
480 /rs_xr="KEGG; ecd:ECDH10B_0003; -."<br />
481 /rs_xr="HOGENOM; HBG646290; -."<br />
482 /rs_xr="OMA; GSAHADN; -."<br />
483 /rs_xr="ProtClustDB; PRK01212; -."<br />
484 /rs_xr="BioCyc; ECOL316385:ECDH10B_0003-MONOMER; -."<br />
485 /rs_xr="GO; GO:0005737; C:cytoplasm;<br />
486 IEA:UniProtKB-SubCell."<br />
487 /rs_xr="GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW."<br />
488 /rs_xr="GO; GO:0004413; F:homoserine kinase activity;<br />
489 IEA:EC."<br />
490 /rs_xr="GO; GO:0009088; P:threonine biosynthetic process;<br />
491 IEA:UniProtKB-KW."<br />
492 /rs_xr="HAMAP; MF_00384; Homoser_kinase; 1; -."<br />
493 /rs_xr="InterPro; IPR006204; GHMP_kinase."<br />
494 /rs_xr="InterPro; IPR013750; GHMP_kinase_C."<br />
495 /rs_xr="InterPro; IPR006203; GHMP_knse_ATP-bd_CS."<br />
496 /rs_xr="InterPro; IPR000870; Homoserine_kin."<br />
497 /rs_xr="InterPro; IPR020568; Ribosomal_S5_D2-typ_fold."<br />
498 /rs_xr="InterPro; IPR014721;<br />
499 Ribosomal_S5_D2-typ_fold_subgr."<br />
500 /rs_xr="Gene3D; G3DSA:3.30.230.10;<br />
501 Ribosomal_S5_D2-type_fold; 1."<br />
502 /rs_xr="Pfam; PF08544; GHMP_kinases_C; 1."<br />
503 /rs_xr="Pfam; PF00288; GHMP_kinases_N; 1."<br />
504 /rs_xr="PIRSF; PIRSF000676; Homoser_kin; 1."<br />
505 /rs_xr="PRINTS; PR00958; HOMSERKINASE."<br />
506 /rs_xr="SUPFAM; SSF54211; Ribosomal_S5_D2-typ_fold; 1."<br />
507 /rs_xr="TIGRFAMs; TIGR00191; thrB; 1."<br />
508 /rs_xr="PROSITE; PS00627; GHMP_KINASES_ATP; 1."<br />
509 /transl_table="11"<br />
510 /translation="MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETF<br />
511 SLNNLGRFADKLPSEPRENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACS<br />
512 VVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDI<br />
513 ISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQ<br />
514 PELAAKLMKDVIAEPYRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPETA<br />
515 QRVADWLGKNYLQNQEGFVHICRLDTAGARVLEN"<br />
516 <br />
517 <font color="red">[Part of this file has been deleted for brevity]</font><br />
518 <br />
519 4639201 gcgcagtcgg gcgaaatatc attactacgc cacgccagtt gaactggtgc cgctgttaga<br />
520 4639261 ggaaaaatct tcatggatga gccatgccgc gctggtgttt ggtcgcgaag attccgggtt<br />
521 4639321 gactaacgaa gagttagcgt tggctgacgt tcttactggt gtgccgatgg tggcggatta<br />
522 4639381 tccttcgctc aatctggggc aggcggtgat ggtctattgc tatcaattag caacattaat<br />
523 4639441 acaacaaccg gcgaaaagtg atgcaacggc agaccaacat caactgcaag ctttacgcga<br />
524 4639501 acgagccatg acattgctga cgactctggc agtggcagat gacataaaac tggtcgactg<br />
525 4639561 gttacaacaa cgcctggggc ttttagagca acgagacacg gcaatgttgc accgtttgct<br />
526 4639621 gcatgatatt gaaaaaaata tcaccaaata aaaaacgcct tagtaagtat ttttc<br />
527 //<br />
528 </td></tr></table>
529
530 </p>
531
532 <h2>Data files</h2>
533
534 <p>
535 None.
536 </p>
537
538 <h2>Notes</h2>
539
540 <p>
541 None.
542 </p>
543
544 <h2>References</h2>
545
546 <pre>
547 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
548 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
549 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
550
551 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
552 large-scale analysis of high-throughput omics data, J. Pest Sci.,
553 31, 7.
554
555 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
556 Analysis Environment with REST and SOAP Web Service Interfaces,
557 Nucleic Acids Res., 38, W700-W705.
558
559 </pre>
560
561 <h2>Warnings</h2>
562
563 <p>
564 None.
565 </p>
566
567 <h2>Diagnostic Error Messages</h2>
568
569 <p>
570 None.
571 </p>
572
573 <h2>Exit status</h2>
574
575 <p>
576 It always exits with a status of 0.
577 </p>
578
579 <h2>Known bugs</h2>
580
581 <p>
582 None.
583 </p>
584
585 <h2>See also</h2>
586
587 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
588 <th>Description</th></tr>
589
590 <tr>
591 <td><a href="entret">entret</a></td>
592 <td>Retrieve sequence entries from flatfile databases and files</td>
593 </tr><tr>
594 <td><a href="seqret">seqret</a></td>
595 <td>Read and write (return) sequences</td>
596 </tr>
597
598 </table>
599
600 <h2>Author(s)</h2>
601
602 <pre>
603 Hidetoshi Itaya (celery@g-language.org)
604 Institute for Advanced Biosciences, Keio University
605 252-0882 Japan
606
607 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
608 Institute for Advanced Biosciences, Keio University
609 252-0882 Japan</pre>
610
611 <h2>History</h2>
612
613 2012 - Written by Hidetoshi Itaya
614
615 <h2>Target users</h2>
616
617 This program is intended to be used by everyone and everything, from
618 naive users to embedded scrips.
619
620 <h2>Comments</h2>
621
622 None.
623
624
625 </HTML>
626
627 <!-- tfm output ends here -->
628 </div>
629 </body>
630 </html>