showorf 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 Display a nucleotide sequence and translation in pretty format Description showorf writes an input nucleotide sequence and its protein translation to an output file in a clear format that is suitable for publication. The translation can be done in any frame or combination of frames using an (optionally) specified genetic code. Usage Here is a sample session with showorf % showorf Display a nucleotide sequence and translation in pretty format Input nucleotide sequence: tembl:x13776 Select Frames To Translate 0 : None 1 : F1 2 : F2 3 : F3 4 : R1 5 : R2 6 : R3 Select one or more values [1,2,3,4,5,6]: Output file [x13776.showorf]: Go to the input files for this example Go to the output files for this example Command line arguments Display a nucleotide sequence and translation in pretty format Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] sequence Nucleotide sequence filename and optional format, or reference (input USA) -frames menu [1,2,3,4,5,6] Select one or more values (Values: 0 (None); 1 (F1); 2 (F2); 3 (F3); 4 (R1); 5 (R2); 6 (R3)) [-outfile] outfile [*.showorf] Output file name Additional (Optional) qualifiers: -table menu [0] Genetic code to use (Values: 0 (Standard); 1 (Standard (with alternative initiation codons)); 2 (Vertebrate Mitochondrial); 3 (Yeast Mitochondrial); 4 (Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma); 5 (Invertebrate Mitochondrial); 6 (Ciliate Macronuclear and Dasycladacean); 9 (Echinoderm Mitochondrial); 10 (Euplotid Nuclear); 11 (Bacterial); 12 (Alternative Yeast Nuclear); 13 (Ascidian Mitochondrial); 14 (Flatworm Mitochondrial); 15 (Blepharisma Macronuclear); 16 (Chlorophycean Mitochondrial); 21 (Trematode Mitochondrial); 22 (Scenedesmus obliquus); 23 (Thraustochytrium Mitochondrial)) -[no]ruler boolean [Y] Add a ruler -[no]plabel boolean [Y] Number translations -[no]nlabel boolean [Y] Number DNA sequence Advanced (Unprompted) qualifiers: -width integer [50] Width of screen (Integer 10 or more) Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of the sequence to be used -send1 integer End of the sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -odirectory2 string Output directory 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 showorf reads a single nucleotide sequence. The input is a standard EMBOSS sequence query (also known as a 'USA'). Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application. The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug. See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats. Input files for usage example 'tembl:x13776' is a sequence entry in the example nucleic acid database 'tembl' Database entry: tembl:x13776 ID X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP. XX AC X13776; M43175; XX DT 19-APR-1989 (Rel. 19, Created) DT 14-NOV-2006 (Rel. 89, Last updated, Version 24) XX DE Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation XX KW aliphatic amidase regulator; amiC gene; amiR gene. XX OS Pseudomonas aeruginosa OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; OC Pseudomonadaceae; Pseudomonas. XX RN [1] RP 1167-2167 RA Rice P.M.; RT ; RL Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases. RL Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG. XX RN [2] RP 1167-2167 RX DOI; 10.1016/0014-5793(89)80249-2. RX PUBMED; 2495988. RA Lowe N., Rice P.M., Drew R.E.; RT "Nucleotide sequence of the aliphatic amidase regulator gene (amiR) of RT Pseudomonas aeruginosa"; RL FEBS Lett. 246(1-2):39-43(1989). XX RN [3] RP 1-1292 RX PUBMED; 1907262. RA Wilson S., Drew R.; RT "Cloning and DNA sequence of amiC, a new gene regulating expression of the RT Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC RT product"; RL J. Bacteriol. 173(16):4914-4921(1991). XX RN [4] RP 1-2167 RA Rice P.M.; RT ; RL Submitted (04-SEP-1991) to the EMBL/GenBank/DDBJ databases. RL Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG. XX DR GOA; Q51417. DR InterPro; IPR003211; AmiSUreI_transpt. DR UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE. [Part of this file has been deleted for brevity] FT /replace="" FT /note="ClaI fragment deleted in pSW36, constitutive FT phenotype" FT misc_feature 1 FT /note="last base of an XhoI site" FT misc_feature 648..653 FT /note="end of 658bp XhoI fragment, deletion in pSW3 causes FT constitutive expression of amiE" FT conflict 1281 FT /replace="g" FT /citation=[3] XX SQ Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other; ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat 60 ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac 120 aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg 180 aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg 240 agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc 300 ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg 360 tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg 420 agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga 480 acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga 540 ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa 600 gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct 660 acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg 720 cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg 780 ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg 840 aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt 900 acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct 960 tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc 1020 tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt 1080 acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca 1140 gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc 1200 agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt 1260 ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg 1320 cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca 1380 gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt 1440 gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc 1500 gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc 1560 cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga 1620 tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa 1680 gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca 1740 ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct 1800 gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg 1860 aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt 1920 catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg 1980 gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct 2040 gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa 2100 ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt 2160 cctcgag 2167 // Output file format As a sequence with high GC content (from Pseudomonas aeruginosa) X13776 has several overlapping open reading frames. The true ORFs are 1..109 (amiB partial) 135..1292 (amiC) 1289..1879 (amiR) 1925..end (amiS partial) Output files for usage example File: x13776.showorf SHOWORF of X13776 from 1 to 2167 ---------|---------|---------|---------|---------| 1 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacggga 50 F1 1 G T A G R A S A R S P P A G R R E 17 F2 1 V P L A E H L L D H H Q P G D G N 17 F3 1 Y R W P S I C S I T T S R A T G 16 R1 9 T G S A S C R S S * W W G P S P 5 R2 106 Y R Q G L M Q E I V V L R A V P 91 R3 38 V A P R A D A R D G G A P R R S 23 ---------|---------|---------|---------|---------| 51 actgcacgatctacctggcgagcctggagcacgagcgggttcgcttcgta 100 F1 18 L H D L P G E P G A R A G S L R T 34 F2 18 C T I Y L A S L E H E R V R F V 33 F3 17 T A R S T W R A W S T S G F A S Y 33 R1 4 F Q V I * R A L R S C S R T R K T 31 R2 90 V A R D V Q R A Q L V L P N A E Y 74 R3 22 S C S R G P S G P A R A P E S R 7 ---------|---------|---------|---------|---------| 101 cggcgctgagcgacagtcacaggagaggaaacggatgggatcgcaccagg 150 F1 35 A L S D S H R R G N G W D R T R 50 F2 34 R R * A T V T G E E T D G I A P G 14 F3 34 G A E R Q S Q E R K R M G S H Q E 50 R1 30 R R Q A V T V P S S V S P I A G P 14 R2 73 P A S R C D C S L F R I P D C W 58 R3 6 V A S L S L * L L P F P H S R V L 398 ---------|---------|---------|---------|---------| 151 agcggccgctgatcggcctgctgttctccgaaaccggcgtcaccgccgat 200 F1 51 S G R * S A C C S P K P A S P P I 13 F2 15 A A A D R P A V L R N R R H R R Y 31 F3 51 R P L I G L L F S E T G V T A D 66 R1 13 A A A S R G A T R R F R R * R R 49 R2 57 S R G S I P R S N E S V P T V A S 41 R3 397 L P R Q D A Q Q E G F G A D G G I 381 ---------|---------|---------|---------|---------| 201 atcgagcgctcgcacgcgtatggcgcattgctcgcggtcgagcaactgaa 250 F1 14 S S A R T R M A H C S R S S N * T 1 F2 32 R A L A R V W R I A R G R A T E 47 F3 67 I E R S H A Y G A L L A V E Q L N 83 R1 48 Y R A S A R T H R M A R P R A V S 32 R2 40 I S R E C A Y P A N S A T S C S F 24 R3 380 D L A R V R I A C Q E R D L L Q 365 ---------|---------|---------|---------|---------| 251 ccgcgagggcggcgtcggcggtcgcccgatcgaaacgctgtcccaggacc 300 F1 2 A R A A S A V A R S K R C P R T 17 [Part of this file has been deleted for brevity] F2 8 N N K R G I V I M L G L V L L Y V 24 F3 22 I T R G V S S S C W D W F C C T L 38 R1 53 L L L L P I T M M S P S T R S Y T 37 R2 73 I V L P T D D D H Q S Q N Q Q V 58 R3 7 C Y C S P Y R * * A P V P E A T R 7 ---------|---------|---------|---------|---------| 1951 tggcgcggtgctgtttctcaatgccgtctggttgctgggcaagatcagcg 2000 F1 16 W R G A V S Q C R L V A G Q D Q R 32 F2 25 G A V L F L N A V W L L G K I S G 41 F3 39 A R C C F S M P S G C W A R S A 54 R1 36 P A T S N R L A T Q N S P L I L 21 R2 57 N A R H Q K E I G D P Q Q A L D A 41 R3 6 Q R P A T E * H R R T A P C S * R 7 ---------|---------|---------|---------|---------| 2001 gtcgggaggtggcggtgatcaacttcctggtcggcgtgctgagcgcctgc 2050 F1 33 S G G G G D Q L P G R R A E R L R 49 F2 42 R E V A V I N F L V G V L S A C 57 F3 55 V G R W R * S T S W S A C * A P A 3 R1 20 P R S T A T I L K R T P T S L A Q 4 R2 40 T P L H R H D V E Q D A H Q A G A 24 R3 6 D P P P P S * S G P R R A S R R 28 ---------|---------|---------|---------|---------| 2051 gtcgcgttctacctgatcttttccgcagcagccgggcagggctcgctgaa 2100 F1 50 R V L P D L F R S S R A G L A E 65 F2 58 V A F Y L I F S A A A G Q G S L K 74 F3 4 S R S T * S F P Q Q P G R A R * R 1 R1 3 T A N * R I K E A A A P C P E S F 12 R2 23 D R E V Q D K G C C G P L A R Q 8 R3 27 R R T R G S R K R L L R A P S A S 11 ---------|---------|---------|---------|---------| 2101 ggccggagcgctgaccctgctattcgcttttacctatctgtgggtggccg 2150 F1 66 G R S A D P A I R F Y L S V G G R 82 F2 75 A G A L T L L F A F T Y L W V A A 91 F3 2 P E R * P C Y S L L P I C G W P 12 R1 11 A P A S V R S N A K V * R H T A 7 R2 7 L G S R Q G Q * E S K G I Q P H G 7 R3 10 P R L A S G A I R K * R D T P P R 6 ---------|------- 2151 ccaaccagttcctcgag 2167 F1 83 Q P V P R 87 F2 92 N Q F L E 96 F3 13 P T S S S 17 R1 6 A L W N R S 1 R2 6 G V L E E L 1 R3 5 W G T G R 1 Data files Showorf uses a genetic code table to translate the sequence. Notes None. References None. Warnings None. Diagnostic Error Messages None. Exit status It exits with a status of 0. It always exits with status 0. Known bugs None. See also Program name Description backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence backtranseq Back-translate a protein sequence to a nucleotide sequence checktrans Reports STOP codons and ORF statistics of a protein coderet Extract CDS, mRNA and translations from feature tables getorf Finds and extracts open reading frames (ORFs) marscan Finds matrix/scaffold recognition (MRS) signatures in DNA sequences plotorf Plot potential open reading frames in a nucleotide sequence prettyseq Write a nucleotide sequence and its translation to file remap Display restriction enzyme binding sites in a nucleotide sequence showseq Displays sequences with features in pretty format sixpack Display a DNA sequence with 6-frame translation and ORFs syco Draw synonymous codon usage statistic plot for a nucleotide sequence tcode Identify protein-coding regions using Fickett TESTCODE statistic transeq Translate nucleic acid sequences wobble Plot third base position variability in a nucleotide sequence Author(s) Alan Bleasby 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 1999 - written - Alan Bleasby Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None