|   | refseqget | 
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| % 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
| 
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
 | 
| Qualifier | Type | Description | Allowed values | Default | 
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-refsequence] (Parameter 1) | refseq | (no help text) refseq value | Reference sequence | |
| [-outfile] (Parameter 2) | outrefseq | (no help text) outrefseq value | Reference sequence | |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-refsequence" associated refseq qualifiers | ||||
| -iformat1 -iformat_refsequence | string | Input reference sequence format | Any string | |
| -iquery1 -iquery_refsequence | string | Input query fields or ID list | Any string | |
| -ioffset1 -ioffset_refsequence | integer | Input start position offset | Any integer value | 0 | 
| -idbname1 -idbname_refsequence | string | User-provided database name | Any string | |
| "-outfile" associated outrefseq qualifiers | ||||
| -odirectory2 -odirectory_outfile | string | Output directory | Any string | |
| -oformat2 -oformat_outfile | string | Referece sequence output format | Any string | |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | 
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | 
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | 
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | 
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | 
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | 
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | 
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | 
| -error | boolean | Report errors | Boolean value Yes/No | Y | 
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | 
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | 
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | 
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.
| 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)) // | 
The output is a standard EMBOSS reference sequence.
The major reference sequence formats are the most common sequence formats.
| 
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
//
 | 
| 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 | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.