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