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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:6.5.6.0
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
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| 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
//
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| 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.