prettyseq 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 Write a nucleotide sequence and its translation to file Description prettyseq reads a nucleotide sequence and writes an output file containing in a clean format the sequence with the translation (within specified ranges) displayed beneath it. The translated nucleic acid region is given lower-case letters with the rest of the input sequence left in the input case. A specified codon usage table is used to translate the codons. Usage Here is a sample session with prettyseq % prettyseq Write a nucleotide sequence and its translation to file Input nucleotide sequence: tembl:x13776 Range(s) to translate [1-2167]: 135-1292 Output file [x13776.prettyseq]: Go to the input files for this example Go to the output files for this example Command line arguments Write a nucleotide sequence and its translation to file Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] sequence Nucleotide sequence filename and optional format, or reference (input USA) -range range [Whole sequence] Range(s) to translate [-outfile] outfile [*.prettyseq] 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 [60] 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 prettyseq reads one or more nucleotide sequences. 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 // You can specify a file of ranges to extract by giving the '-range' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-range @myfile'). The format of the range file is: * Comment lines start with '#' in the first column. * Comment lines and blank lines are ignored. * The line may start with white-space. * There are two positive (integer) numbers per line separated by one or more space or TAB characters. * The second number must be greater or equal to the first number. * There can be optional text after the two numbers to annotate the line. * White-space before or after the text is removed. An example range file is: # this is my set of ranges 12 23 4 5 this is like 12-23, but smaller 67 10348 interesting region Output file format Output files for usage example File: x13776.prettyseq PRETTYSEQ of X13776 from 1 to 2167 ---------|---------|---------|---------|---------|---------| 1 GGTACCGCTGGCCGAGCATCTGCTCGATCACCACCAGCCGGGCGACGGGAACTGCACGAT 60 ---------|---------|---------|---------|---------|---------| 61 CTACCTGGCGAGCCTGGAGCACGAGCGGGTTCGCTTCGTACGGCGCTGAGCGACAGTCAC 120 ---------|---------|---------|---------|---------|---------| 121 AGGAGAGGAAACGGatgggatcgcaccaggagcggccgctgatcggcctgctgttctccg 180 1 M G S H Q E R P L I G L L F S E 16 ---------|---------|---------|---------|---------|---------| 181 aaaccggcgtcaccgccgatatcgagcgctcgcacgcgtatggcgcattgctcgcggtcg 240 17 T G V T A D I E R S H A Y G A L L A V E 36 ---------|---------|---------|---------|---------|---------| 241 agcaactgaaccgcgagggcggcgtcggcggtcgcccgatcgaaacgctgtcccaggacc 300 37 Q L N R E G G V G G R P I E T L S Q D P 56 ---------|---------|---------|---------|---------|---------| 301 ccggcggcgacccggaccgctatcggctgtgcgccgaggacttcattcgcaaccgggggg 360 57 G G D P D R Y R L C A E D F I R N R G V 76 ---------|---------|---------|---------|---------|---------| 361 tacggttcctcgtgggctgctacatgtcgcacacgcgcaaggcggtgatgccggtggtcg 420 77 R F L V G C Y M S H T R K A V M P V V E 96 ---------|---------|---------|---------|---------|---------| 421 agcgcgccgacgcgctgctctgctacccgaccccctacgagggcttcgagtattcgccga 480 97 R A D A L L C Y P T P Y E G F E Y S P N 116 ---------|---------|---------|---------|---------|---------| 481 acatcgtctacggcggtccggcgccgaaccagaacagtgcgccgctggcggcgtacctga 540 117 I V Y G G P A P N Q N S A P L A A Y L I 136 ---------|---------|---------|---------|---------|---------| 541 ttcgccactacggcgagcgggtggtgttcatcggctcggactacatctatccgcgggaaa 600 137 R H Y G E R V V F I G S D Y I Y P R E S 156 ---------|---------|---------|---------|---------|---------| 601 gcaaccatgtgatgcgccacctgtatcgccagcacggcggcacggtgctcgaggaaatct 660 157 N H V M R H L Y R Q H G G T V L E E I Y 176 ---------|---------|---------|---------|---------|---------| 661 acattccgctgtatccctccgacgacgacttgcagcgcgccgtcgagcgcatctaccagg 720 177 I P L Y P S D D D L Q R A V E R I Y Q A 196 [Part of this file has been deleted for brevity] 1441 GCCGGTGGACGTGGTCTTCACCAGCATTTTCCAGAATGGCCACCACGACGAGATCGCTGC 1500 ---------|---------|---------|---------|---------|---------| 1501 GCTGCTCGCCGCCGGGACTCCGCGCACTACCCTGGTGGCGCTGGTGGAGTACGAAAGCCC 1560 ---------|---------|---------|---------|---------|---------| 1561 CGCGGTGCTCTCGCAGATCATCGAGCTGGAGTGCCACGGCGTGATCACCCAGCCGCTCGA 1620 ---------|---------|---------|---------|---------|---------| 1621 TGCCCACCGGGTGCTGCCTGTGCTGGTATCGGCGCGGCGCATCAGCGAGGAAATGGCGAA 1680 ---------|---------|---------|---------|---------|---------| 1681 GCTGAAGCAGAAGACCGAGCAGCTCCAGGACCGCATCGCCGGCCAGGCCCGGATCAACCA 1740 ---------|---------|---------|---------|---------|---------| 1741 GGCCAAGGTGTTGCTGATGCAGCGCCATGGCTGGGACGAGCGCGAGGCGCACCAGCACCT 1800 ---------|---------|---------|---------|---------|---------| 1801 GTCGCGGGAAGCGATGAAGCGGCGCGAGCCGATCCTGAAGATCGCTCAGGAGTTGCTGGG 1860 ---------|---------|---------|---------|---------|---------| 1861 AAACGAGCCGTCCGCCTGAGCGATCCGGGCCGACCAGAACAATAACAAGAGGGGTATCGT 1920 ---------|---------|---------|---------|---------|---------| 1921 CATCATGCTGGGACTGGTTCTGCTGTACGTTGGCGCGGTGCTGTTTCTCAATGCCGTCTG 1980 ---------|---------|---------|---------|---------|---------| 1981 GTTGCTGGGCAAGATCAGCGGTCGGGAGGTGGCGGTGATCAACTTCCTGGTCGGCGTGCT 2040 ---------|---------|---------|---------|---------|---------| 2041 GAGCGCCTGCGTCGCGTTCTACCTGATCTTTTCCGCAGCAGCCGGGCAGGGCTCGCTGAA 2100 ---------|---------|---------|---------|---------|---------| 2101 GGCCGGAGCGCTGACCCTGCTATTCGCTTTTACCTATCTGTGGGTGGCCGCCAACCAGTT 2160 ------- 2161 CCTCGAG 2167 Data files The codon usage table is read by default from "Ehum.cut" in the 'data/CODONS' directory of the EMBOSS distribution. If the name of a codon usage file is specified on the command line, then this file will first be searched for in the current directory and then in the 'data/CODONS' directory of the EMBOSS distribution. 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 Notes By default, the base and residue numbers of the sequence and its translation are shown beside the sequences in the output. There are options to change this behaviour. The translation will be shown in a number of sequence regions only. The ranges are specified with the -range qualifier. As an alternative to specifying a set of ranges at the command-line, a range file containing such range data may be specified (see "Input File Format"). References None. Warnings None. Diagnostic Error Messages "Range outside length of sequence" - this is self explanatory. You should specify a range of sequences to translate that is within the length of the input sequence. Exit status It always exits with a status of 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 iep Calculate the isoelectric point of proteins lindna Draws linear maps of DNA constructs 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 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 sixpack Display a DNA sequence with 6-frame translation and ORFs transeq Translate nucleic acid sequences showseq has more options for specifying various ways of displaying a sequence, with or without various ways of translating it. 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 Written (1999) - Alan Bleasby Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None