% refseqget -of embl 
Get reference sequence
-refsequence : enter refseq value: tembl:em498477
Reference sequence output file [em498477.embl]: test.out

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

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))
//

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
//