sixpack 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 DNA sequence with 6-frame translation and ORFs Description sixpack reads a DNA sequence and writes an output file giving out the forward and reverse sense sequences with the three forward and (optionally) three reverse translations in a pretty display format. A genetic code may be specified for the translation. There are various options to control the appearance of the output file. It also writes a file of protein sequences corresponding to any open reading frames that are larger than the specified minimum size: the default of 1 base shows all possible open reading frames. Algorithm The program takes the following steps: The nucleic acid sequence is read in. The required genetic code is read in from the EGC* data files. The three forward and three reverse translations are created. The name and description are written to the output display file. Any required regions to be changed to upper case are changed. Any required regions to be highlighted in HTML colour tags are changed. The reverse sense sequence is placed below the forward sequence. The forward translations are placed above the sequences. The reverse translation are placed below the sequences. The display is written out, split at the ends of lines. Any ORFs that are longer than the specified minimum size are written to the out put sequence file. Usage Here is a sample session with sixpack % sixpack Display a DNA sequence with 6-frame translation and ORFs Input nucleotide sequence: tembl:x13776 Output file [x13776.sixpack]: protein output sequence(s) [x13776.fasta]: Go to the input files for this example Go to the output files for this example Command line arguments Display a DNA sequence with 6-frame translation and ORFs Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] sequence Nucleotide sequence filename and optional format, or reference (input USA) [-outfile] outfile [*.sixpack] Output file name -outseq seqoutall [.] ORF sequence output Additional (Optional) qualifiers: -table menu [0] Genetics code used for the translation (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]firstorf boolean [Y] Count the beginning of a sequence as a possible ORF, even if it's inferior to the minimal ORF size. -[no]lastorf boolean [Y] Count the end of a sequence as a possible ORF, even if it's not finishing with a STOP, or inferior to the minimal ORF size. -mstart boolean [N] Displays only ORFs starting with an M. Advanced (Unprompted) qualifiers: -[no]reverse boolean [Y] Display also the translation of the DNA sequence in the 3 reverse frames -orfminsize integer [1] Minimum size of Open Reading Frames (ORFs) to display in the translations. (Integer 1 or more) -uppercase range [If this is left blank, then the sequence case is left alone.] Regions to put in uppercase. If this is left blank, then the sequence case is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99 -highlight range [(full sequence)] Regions to colour if formatting for HTML. If this is left blank, then the sequence is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are followed by any valid HTML font colour. Examples of region specifications are: 24-45 blue 56-78 orange 1-100 green 120-156 red A file of ranges to colour (one range per line) can be specified as '@filename'. -[no]number boolean [Y] Number the sequence at the beginning and the end of each line. -width integer [60] Number of nucleotides displayed on each line (Integer 1 or more) -length integer [0] Line length of page (0 for indefinite) (Integer 0 or more) -margin integer [10] Margin around sequence for numbering. (Integer 0 or more) -[no]name boolean [Y] Set this to be false if you do not wish to display the ID name of the sequence. -[no]description boolean [Y] Set this to be false if you do not wish to display the description of the sequence. -offset integer [1] Number from which you want the DNA sequence to be numbered. (Any integer value) -html boolean [N] Use HTML formatting 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 "-outseq" associated qualifiers -osformat string Output seq format -osextension string File name extension -osname string Base file name -osdirectory string Output directory -osdbname string Database name to add -ossingle boolean Separate file for each entry -oufo string UFO features -offormat string Features format -ofname string Features file name -ofdirectory 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 sixpack 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 sixpack writes a text report and an ORF sequence file. The output is a standard EMBOSS sequence file. The results can be output in one of several styles by using the command-line qualifier -osformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq. See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats. Output files for usage example File: x13776.sixpack X13776 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation G T A G R A S A R S P P A G R R E L H D F1 V P L A E H L L D H H Q P G D G N C T I F2 Y R W P S I C S I T T S R A T G T A R S F3 1 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat 60 ----:----|----:----|----:----|----:----|----:----|----:----| 1 ccatggcgaccggctcgtagacgagctagtggtggtcggcccgctgcccttgacgtgcta 60 P V A P R A D A R D G G A P R R S S C S F6 X Y R Q G L M Q E I V V L R A V P V A R F5 T G S A S C R S S * W W G P S P F Q V I F4 L P G E P G A R A G S L R T A L S D S H F1 Y L A S L E H E R V R F V R R * A T V T F2 T W R A W S T S G F A S Y G A E R Q S Q F3 61 ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac 120 ----:----|----:----|----:----|----:----|----:----|----:----| 61 gatggaccgctcggacctcgtgctcgcccaagcgaagcatgccgcgactcgctgtcagtg 120 R G P S G P A R A P E S R V A S L S L * F6 D V Q R A Q L V L P N A E Y P A S R C D F5 * R A L R S C S R T R K T R R Q A V T V F4 R R G N G W D R T R S G R * S A C C S P F1 G E E T D G I A P G A A A D R P A V L R F2 E R K R M G S H Q E R P L I G L L F S E F3 121 aggagaggaaacggatgggatcgcaccaggagcggccgctgatcggcctgctgttctccg 180 ----:----|----:----|----:----|----:----|----:----|----:----| 121 tcctctcctttgcctaccctagcgtggtcctcgccggcgactagccggacgacaagaggc 180 L L P F P H S R V L L P R Q D A Q Q E G F6 C S L F R I P D C W S R G S I P R S N E F5 P S S V S P I A G P A A A S R G A T R R F4 K P A S P P I S S A R T R M A H C S R S F1 N R R H R R Y R A L A R V W R I A R G R F2 T G V T A D I E R S H A Y G A L L A V E F3 181 aaaccggcgtcaccgccgatatcgagcgctcgcacgcgtatggcgcattgctcgcggtcg 240 ----:----|----:----|----:----|----:----|----:----|----:----| 181 tttggccgcagtggcggctatagctcgcgagcgtgcgcataccgcgtaacgagcgccagc 240 F G A D G G I D L A R V R I A C Q E R D F6 S V P T V A S I S R E C A Y P A N S A T F5 F R R * R R Y R A S A R T H R M A R P R F4 S N * T A R A A S A V A R S K R C P R T F1 [Part of this file has been deleted for brevity] 1981 caacgacccgttctagtcgccagccctccaccgccactagttgaaggaccagccgcacga 2040 T A P C S * R D P P P P S * S G P R R A F6 P Q Q A L D A T P L H R H D V E Q D A H F5 N S P L I L P R S T A T I L K R T P T S F4 E R L R R V L P D L F R S S R A G L A E F1 S A C V A F Y L I F S A A A G Q G S L K F2 A P A S R S T * S F P Q Q P G R A R * R F3 2041 gagcgcctgcgtcgcgttctacctgatcttttccgcagcagccgggcagggctcgctgaa 2100 ----:----|----:----|----:----|----:----|----:----|----:----| 2041 ctcgcggacgcagcgcaagatggactagaaaaggcgtcgtcggcccgtcccgagcgactt 2100 S R R R R T R G S R K R L L R A P S A S F6 Q A G A D R E V Q D K G C C G P L A R Q F5 L A Q T A N * R I K E A A A P C P E S F F4 G R S A D P A I R F Y L S V G G R Q P V F1 A G A L T L L F A F T Y L W V A A N Q F F2 P E R * P C Y S L L P I C G W P P T S S F3 2101 ggccggagcgctgaccctgctattcgcttttacctatctgtgggtggccgccaaccagtt 2160 ----:----|----:----|----:----|----:----|----:----|----:----| 2101 ccggcctcgcgactgggacgataagcgaaaatggatagacacccaccggcggttggtcaa 2160 P R L A S G A I R K * R D T P P R W G T F6 L G S R Q G Q * E S K G I Q P H G G V L F5 A P A S V R S N A K V * R H T A A L W N F4 P R X F1 L E F2 S X F3 2161 cctcgag 2167 ----:-- 2161 ggagctc 2220 G R F6 E E L F5 R S F4 ############################## Minimum size of ORFs : 1 Total ORFs in frame 1 : 8 Total ORFs in frame 2 : 5 Total ORFs in frame 3 : 13 Total ORFs in frame 4 : 10 Total ORFs in frame 5 : 16 Total ORFs in frame 6 : 15 Total ORFs : 67 ############################## File: x13776.fasta >X13776_1_ORF1 Translation of X13776 in frame 1, ORF 1, threshold 1, 53aa GTAGRASARSPPAGRRELHDLPGEPGARAGSLRTALSDSHRRGNGWDRTRSGR >X13776_1_ORF2 Translation of X13776 in frame 1, ORF 2, threshold 1, 28aa SACCSPKPASPPISSARTRMAHCSRSSN >X13776_1_ORF3 Translation of X13776 in frame 1, ORF 3, threshold 1, 52aa TARAASAVARSKRCPRTPAATRTAIGCAPRTSFATGGYGSSWAATCRTRARR >X13776_1_ORF4 Translation of X13776 in frame 1, ORF 4, threshold 1, 43aa CRWSSAPTRCSATRPPTRASSIRRTSSTAVRRRTRTVRRWRRT >X13776_1_ORF5 Translation of X13776 in frame 1, ORF 5, threshold 1, 23aa FATTASGWCSSARTTSIRGKATM >X13776_1_ORF6 Translation of X13776 in frame 1, ORF 6, threshold 1, 72aa CATCIASTAARCSRKSTFRCIPPTTTCSAPSSASTRRAPTWSSPPWWAPAPPSCIAPSPV ATATAGGRRSPA >X13776_1_ORF7 Translation of X13776 in frame 1, ORF 7, threshold 1, 357aa PPARRRWRRWRVTWQRGRWWSRLTSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGR PCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR SAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHERQLAARQPARVAGAGPQPAGGGQRRP GLAADPHRLFGAPVLAAAGSLRRAGGRGLHQHFPEWPPRRDRCAARRRDSAHYPGGAGGV RKPRGALADHRAGVPRRDHPAARCPPGAACAGIGAAHQRGNGEAEAEDRAAPGPHRRPGP DQPGQGVADAAPWLGRARGAPAPVAGSDEAARADPEDRSGVAGKRAVRLSDPGRPEQ >X13776_1_ORF8 Translation of X13776 in frame 1, ORF 8, threshold 1, 88aa QEGYRHHAGTGSAVRWRGAVSQCRLVAGQDQRSGGGGDQLPGRRAERLRRVLPDLFRSSR AGLAEGRSADPAIRFYLSVGGRQPVPRX >X13776_2_ORF1 Translation of X13776 in frame 2, ORF 1, threshold 1, 35aa VPLAEHLLDHHQPGDGNCTIYLASLEHERVRFVRR >X13776_2_ORF2 Translation of X13776 in frame 2, ORF 2, threshold 1, 252aa ATVTGEETDGIAPGAAADRPAVLRNRRHRRYRALARVWRIARGRATEPRGRRRRSPDRNA VPGPRRRPGPLSAVRRGLHSQPGGTVPRGLLHVAHAQGGDAGGRARRRAALLPDPLRGLR VFAEHRLRRSGAEPEQCAAGGVPDSPLRRAGGVHRLGLHLSAGKQPCDAPPVSPARRHGA RGNLHSAVSLRRRLAARRRAHLPGARRRGLLHRGGHRHRRAVSRHRPSLRRRQAAADRQP DHQRGGGGEDGE >X13776_2_ORF3 Translation of X13776 in frame 2, ORF 3, threshold 1, 125aa RGRGAGGGRALLLQHRYARQPGLRPGLPWFLPGERDHHRLGRGGLLADLVARPRRAGRRQ LAGGRRAAAPVRHRHRRATGAGPGGAPEQPQPPVFAHRGNRCARRVPGPLAVARTDSPRP LCRRA >X13776_2_ORF4 Translation of X13776 in frame 2, ORF 4, threshold 1, 210aa PRRLVRQHGRGTAPMSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPP EAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVI TQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDERE AHQHLSREAMKRREPILKIAQELLGNEPSA >X13776_2_ORF5 Translation of X13776 in frame 2, ORF 5, threshold 1, 96aa AIRADQNNNKRGIVIMLGLVLLYVGAVLFLNAVWLLGKISGREVAVINFLVGVLSACVAF YLIFSAAAGQGSLKAGALTLLFAFTYLWVAANQFLE >X13776_3_ORF1 Translation of X13776 in frame 3, ORF 1, threshold 1, 429aa YRWPSICSITTSRATGTARSTWRAWSTSGFASYGAERQSQERKRMGSHQERPLIGLLFSE TGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGV RFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLI RHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQA RADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPY FSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLY [Part of this file has been deleted for brevity] SEPMNTTRSP >X13776_5_ORF11 Translation of X13776 in frame 5, ORF 11, threshold 1, 19aa WRIRYAASGALFWFGAGPP >X13776_5_ORF12 Translation of X13776 in frame 5, ORF 12, threshold 1, 10aa TMFGEYSKPS >X13776_5_ORF13 Translation of X13776 in frame 5, ORF 13, threshold 1, 3aa GVG >X13776_5_ORF14 Translation of X13776 in frame 5, ORF 14, threshold 1, 20aa QSSASARSTTGITALRVCDM >X13776_5_ORF15 Translation of X13776 in frame 5, ORF 15, threshold 1, 19aa QPTRNRTPRLRMKSSAHSR >X13776_5_ORF16 Translation of X13776 in frame 5, ORF 16, threshold 1, 107aa RSGSPPGSWDSVSIGRPPTPPSRFSCSTASNAPYACERSISAVTPVSENSRPISGRSWCD PIRFLSCDCRSAPYEANPLVLQARQVDRAVPVARLVVIEQMLGQRYX >X13776_6_ORF1 Translation of X13776 in frame 6, ORF 1, threshold 1, 11aa RGTGWRPPTDR >X13776_6_ORF2 Translation of X13776 in frame 6, ORF 2, threshold 1, 36aa KRIAGSALRPSASPARLLRKRSGRTRRRRSARRPGS >X13776_6_ORF3 Translation of X13776 in frame 6, ORF 3, threshold 1, 7aa SPPPPDR >X13776_6_ORF4 Translation of X13776 in frame 6, ORF 4, threshold 1, 8aa SCPATRRH >X13776_6_ORF5 Translation of X13776 in frame 6, ORF 5, threshold 1, 14aa ETAPRQRTAEPVPA >X13776_6_ORF6 Translation of X13776 in frame 6, ORF 6, threshold 1, 61aa RYPSCYCSGRPGSLRRTARFPATPERSSGSARAASSLPATGAGAPRARPSHGAASATPWP G >X13776_6_ORF7 Translation of X13776 in frame 6, ORF 7, threshold 1, 23aa SGPGRRCGPGAARSSASASPFPR >X13776_6_ORF8 Translation of X13776 in frame 6, ORF 8, threshold 1, 18aa CAAPIPAQAAPGGHRAAG >X13776_6_ORF9 Translation of X13776 in frame 6, ORF 9, threshold 1, 8aa SRRGTPAR >X13776_6_ORF10 Translation of X13776 in frame 6, ORF 10, threshold 1, 16aa SARAPRGFRTPPAPPG >X13776_6_ORF11 Translation of X13776 in frame 6, ORF 11, threshold 1, 22aa CAESRRRAAQRSRRGGHSGKCW >X13776_6_ORF12 Translation of X13776 in frame 6, ORF 12, threshold 1, 32aa RPRPPARRRLPAAASTGAPNNRCGSAARPGRR >X13776_6_ORF13 Translation of X13776 in frame 6, ORF 13, threshold 1, 5aa PPPAG >X13776_6_ORF14 Translation of X13776 in frame 6, ORF 14, threshold 1, 407aa GPAPATRAGCRAASWRSWERSPAHAGGPVVEVMHDDIRVGANRFGRLPADLEHAARIDFR DARRQAAVVVLALHPDRPLWRVDVDVVQVPLHVFHPPVACGLRGAAEQQGLPVGRLGPGG DGRVLREETMAGLDEGPAGGRIDAGEVRRDHHLPLCHVTLHLRHLRLAGGQAGDRRPPAV AVATGDGAIQLGGAGAHHGGEDHVGARLVDALDGALQVVVGGIQRNVDFLEHRAAVLAIQ VAHHMVAFPRIDVVRADEHHPLAVVANQVRRQRRTVLVRRRTAVDDVRRILEALVGGRVA EQRVGALDHRHHRLARVRHVAAHEEPYPPVANEVLGAQPIAVRVAAGVLGQRFDRATADA ALAVQLLDREQCAIRVRALDIGGDAGFGEQQADQRPLLVRSHPFPLL >X13776_6_ORF15 Translation of X13776 in frame 6, ORF 15, threshold 1, 39aa LSLSAVRSEPARAPGSPGRSCSSRRPAGGDRADARPAVP Data files EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA. To see the available EMBOSS data files, run: % embossdata -showall To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run: % embossdata -fetch -file Exxx.dat Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata". The directories are searched in the following order: * . (your current directory) * .embossdata (under your current directory) * ~/ (your home directory) * ~/.embossdata The Genetic Code data files are based on the NCBI genetic code tables. Their names and descriptions are: EGC.0 Standard (Differs from GC.1 in that it only has initiation site 'AUG') EGC.1 Standard EGC.2 Vertebrate Mitochodrial EGC.3 Yeast Mitochondrial EGC.4 Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma EGC.5 Invertebrate Mitochondrial EGC.6 Ciliate Macronuclear and Dasycladacean EGC.9 Echinoderm Mitochondrial EGC.10 Euplotid Nuclear EGC.11 Bacterial EGC.12 Alternative Yeast Nuclear EGC.13 Ascidian Mitochondrial EGC.14 Flatworm Mitochondrial EGC.15 Blepharisma Macronuclear EGC.16 Chlorophycean Mitochondrial EGC.21 Trematode Mitochondrial EGC.22 Scenedesmus obliquus EGC.23 Thraustochytrium Mitochondrial The format of these files is very simple. It consists of several lines of optional comments, each starting with a '#' character. These are followed the line: 'Genetic Code [n]', where 'n' is the number of the genetic code file. This is followed by the description of the code and then by four lines giving the IUPAC one-letter code of the translated amino acid, the start codons (indicdated by an 'M') and the three bases of the codon, lined up one on top of the other. For example: ------------------------------------------------------------------------------ # Genetic Code Table # # Obtained from: http://www.ncbi.nlm.nih.gov/collab/FT/genetic_codes.html # and: http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c # # Differs from Genetic Code [1] only in that the initiation sites have been # changed to only 'AUG' Genetic Code [0] Standard AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG Starts = -----------------------------------M---------------------------- Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG ------------------------------------------------------------------------------ Notes An open reading frame is defined in this program as any possible translation between two STOP codons. Optionally, the beginning or end of a sequence may be counted as an ORF even if it's less than the minimal ORF size or (end only) lacking a STOP codon. See the -firstorf and -lastorf options. 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 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 cirdna Draws circular maps of DNA constructs coderet Extract CDS, mRNA and translations from feature tables getorf Finds and extracts open reading frames (ORFs) iep Calculate the isoelectric point of proteins lindna Draws linear maps of DNA constructs marscan Finds matrix/scaffold recognition (MRS) signatures in DNA sequences pepinfo Plot amino acid properties of a protein sequence in parallel pepnet Draw a helical net for a protein sequence pepwheel Draw a helical wheel diagram for a protein sequence plotorf Plot potential open reading frames in a nucleotide sequence prettyplot Draw a sequence alignment with pretty formatting prettyseq Write a nucleotide sequence and its translation to file remap Display restriction enzyme binding sites in a nucleotide sequence showfeat Display features of a sequence in pretty format showorf Display a nucleotide sequence and translation in pretty format showpep Displays protein sequences with features in pretty format showseq Displays sequences with features in pretty format 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) Thomas Laurent formerly at: Lion Bioscience Ltd, Compass House, 80-82 Newmarket Road, Cambridge, CB5 8DZ, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Written (November 2002) - Thomas Laurent Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None