showseq 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 Displays sequences with features in pretty format Description showseq displays one or more nucleic acid sequences, with features, in a style suitable for publication. The output is sent to screen by default but can be written to file. You may pick a format from a list, alternatively, use the many options to control what is output and in what format. Optionally, the sequence feature table can be displayed. The sequence can be translated, using the specified genetic code tables. Also recognition sites and/or cut sites of restriction enzymes from the REBASE database may be displayed. There are various other options for controlling how the sequence is displayed and numbered and the output can be formatted for HTML. Usage Here is a sample session with showseq % showseq tembl:x13776 -sbeg 1 -send 100 Displays sequences with features in pretty format Things to display 0 : Enter your own list of things to display 1 : Sequence only 2 : Default sequence with features 3 : Pretty sequence 4 : One frame translation 5 : Three frame translations 6 : Six frame translations 7 : Restriction enzyme map 8 : Baroque Display format [2]: Output file [x13776.showseq]: Go to the input files for this example Go to the output files for this example Example 2 The standard list of output formats are only a small selection of the possible ways in which a sequence might be displayed. Precise control over the output format is acheived by selecting the qualifier '-format 0' (Option 0 in the list of things to display). For example, by choosing format '0' and then specifying that we want to display the things: 'b,s,t,c', we will output the sequence in the following way: % showseq tembl:x13776 -sbeg 1 -send 120 Displays sequences with features in pretty format Things to display 0 : Enter your own list of things to display 1 : Sequence only 2 : Default sequence with features 3 : Pretty sequence 4 : One frame translation 5 : Three frame translations 6 : Six frame translations 7 : Restriction enzyme map 8 : Baroque Display format [2]: 0 Specify your own things to display S : Sequence B : Blank line 1 : Frame1 translation 2 : Frame2 translation 3 : Frame3 translation -1 : CompFrame1 translation -2 : CompFrame2 translation -3 : CompFrame3 translation T : Ticks line N : Number ticks line C : Complement sequence F : Features R : Restriction enzyme cut sites in forward sense -R : Restriction enzyme cut sites in reverse sense A : Annotation Enter a list of things to display [B,N,T,S,A,F]: b,s,t,c Output file [x13776.showseq]: Go to the output files for this example Example 3 Display only the sequence: % showseq tembl:x13776 -sbeg 1 -send 100 -noname -nodesc -format 0 -thing S Displays sequences with features in pretty format Output file [x13776.showseq]: Go to the output files for this example Example 4 Number the sequence lines in the margin: % showseq tembl:x13776 -sbeg 1 -send 100 -format 1 -number Displays sequences with features in pretty format Output file [x13776.showseq]: Go to the output files for this example Example 5 Start the numbering at a specified value ('123' in this case): % showseq tembl:x13776 -sbeg 1 -send 100 -format 1 -number -offset 123 Displays sequences with features in pretty format Output file [x13776.showseq]: Go to the output files for this example Example 6 Make selected regions uppercase. (Use '-slower' to force the rest of the sequence to be lowercase). % showseq tembl:x13776 -sbeg 1 -send 100 -format 1 -slower -upper "8-24,65-81" Displays sequences with features in pretty format Output file [x13776.showseq]: Go to the output files for this example Example 7 Translate selected regions: % showseq tembl:x13776 -sbeg 1 -send 120 -format 5 -trans 25-49,66-76 Displays sequences with features in pretty format Output file [x13776.showseq]: Go to the output files for this example Example 8 Add your own annotation to the display: % showseq tembl:x13776 -sbeg 1 -send 100 -format 2 -send 120 -annotation "13-26 binding site 15-15 SNP" Displays sequences with features in pretty format Output file [x13776.showseq]: Go to the output files for this example Command line arguments Displays sequences with features in pretty format Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers (* if not always prompted): [-sequence] seqall (Gapped) nucleotide sequence(s) filename and optional format, or reference (input USA) -format menu [2] Display format (Values: 0 (Enter your own list of things to display); 1 (Sequence only); 2 (Default sequence with features); 3 (Pretty sequence); 4 (One frame translation); 5 (Three frame translations); 6 (Six frame translations); 7 (Restriction enzyme map); 8 (Baroque)) * -things menu [B,N,T,S,A,F] Specify a list of one or more code characters in the order in which you wish things to be displayed one above the other down the page. For example if you wish to see things displayed in the order: sequence, complement sequence, ticks line, frame 1 translation, blank line; then you should enter 'S,C,T,1,B'. (Values: S (Sequence); B (Blank line); 1 (Frame1 translation); 2 (Frame2 translation); 3 (Frame3 translation); -1 (CompFrame1 translation); -2 (CompFrame2 translation); -3 (CompFrame3 translation); T (Ticks line); N (Number ticks line); C (Complement sequence); F (Features); R (Restriction enzyme cut sites in forward sense); -R (Restriction enzyme cut sites in reverse sense); A (Annotation)) [-outfile] outfile [*.showseq] Output file name Additional (Optional) qualifiers: -translate range [If this is left blank the complete sequence is translated.] Regions to translate (if translating). If this is left blank the complete sequence is translated. 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 -revtranslate range [If this is left blank the complete reverse sequence is translated.] Regions to translate (if translating). If this is left blank the complete sequence is translated. 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: 78-56, 45-24, 888..765, 99=67; 45:1 -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'. -annotation range [If this is left blank, then no annotation is added.] Regions to annotate by marking. If this is left blank, then no annotation is added. A set of regions is specified by a set of pairs of positions followed by optional text. The positions are integers. They are followed by any text (but not digits when on the command-line). Examples of region specifications are: 24-45 new domain 56-78 match to Mouse 1-100 First part 120-156 oligo A file of ranges to annotate (one range per line) can be specified as '@filename'. -enzymes string [all] The name 'all' reads in all enzyme names from the REBASE database. You can specify enzymes by giving their names with commas between then, such as: 'HincII,hinfI,ppiI,hindiii'. The case of the names is not important. You can specify a file of enzyme names to read in by giving the name of the file holding the enzyme names with a '@' character in front of it, for example, '@enz.list'. Blank lines and lines starting with a hash character or '!' are ignored and all other lines are concatenated together with a comma character ',' and then treated as the list of enzymes to search for. An example of a file of enzyme names is: ! my enzymes HincII, ppiII ! other enzymes hindiii HinfI PpiI (Any string) -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)) -sourcematch string [*] By default any feature source in the feature table is shown. You can set this to match any feature source you wish to show. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from. The source may be wildcarded by using '*'. If you wish to show more than one source, separate their names with the character '|', eg: gene* | embl (Any string) -typematch string [*] By default any feature type in the feature table is shown. You can set this to match any feature type you wish to show. See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types. The type may be wildcarded by using '*'. If you wish to show more than one type, separate their names with the character '|', eg: *UTR | intron (Any string) -sensematch integer [0 - any sense, 1 - forward sense, -1 - reverse sense] By default any feature type in the feature table is shown. You can set this to match any feature sense you wish to show. 0 - any sense, 1 - forward sense, -1 - reverse sense (Integer from -1 to 1) -minscore float [0.0] Minimum score of feature to display (see also maxscore) (Any numeric value) -maxscore float [0.0] Maximum score of feature to display. If both minscore and maxscore are zero (the default), then any score is ignored (Any numeric value) -tagmatch string [*] Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Some of these tags also have values, for example '/gene' can have the value of the gene name. By default any feature tag in the feature table is shown. You can set this to match any feature tag you wish to show. The tag may be wildcarded by using '*'. If you wish to show more than one tag, separate their names with the character '|', eg: gene | label (Any string) -valuematch string [*] Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Only some of these tags can have values, for example '/gene' can have the value of the gene name. By default any feature tag value in the feature table is shown. You can set this to match any feature tag value you wish to show. The tag value may be wildcarded by using '*'. If you wish to show more than one tag value, separate their names with the character '|', eg: pax* | 10 (Any string) -stricttags boolean [N] By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed. If this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed. Advanced (Unprompted) qualifiers: -mfile datafile [Emethylsites.dat] Restriction enzyme methylation data file -flatreformat boolean [N] This changes the output format to one where the recognition site is indicated by a row of '===' characters and the cut site is pointed to by a '>' character in the forward sense, or a '<' in the reverse sense strand. -mincuts integer [1] This sets the minimum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut fewer times than this will be ignored. (Integer from 1 to 1000) -maxcuts integer [2000000000] This sets the maximum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut more times than this will be ignored. (Any integer value) -sitelen integer [4] This sets the minimum length of the restriction enzyme recognition site. Any enzymes with sites shorter than this will be ignored. (Integer from 2 to 20) -single boolean [N] If this is set then this forces the values of the mincuts and maxcuts qualifiers to both be 1. Any other value you may have set them to will be ignored. -[no]blunt boolean [Y] This allows those enzymes which cut at the same position on the forward and reverse strands to be considered. -[no]sticky boolean [Y] This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered. -[no]ambiguity boolean [Y] This allows those enzymes which have one or more 'N' ambiguity codes in their pattern to be considered -plasmid boolean [N] If this is set then this allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered. -methylation boolean [N] If this is set then RE recognition sites will not match methylated bases. -[no]commercial boolean [Y] If this is set, then only those enzymes with a commercial supplier will be searched for. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through 'all' the enzymes in the REBASE database. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier. -[no]limit boolean [Y] This limits the reporting of enzymes to just one enzyme from each group of isoschizomers. The enzyme chosen to represent an isoschizomer group is the prototype indicated in the data file 'embossre.equ', which is created by the program 'rebaseextract'. If you prefer different prototypes to be used, make a copy of embossre.equ in your home directory and edit it. If this value is set to be false then all of the input enzymes will be reported. You might like to set this to false if you are supplying an explicit set of enzymes rather than searching 'all' of them. -orfminsize integer [0] This sets the minimum size of Open Reading Frames (ORFs) to display in the translations. All other translation regions are masked by changing the amino acids to '-' characters. (Integer 0 or more) -threeletter boolean [N] Display protein sequences in three-letter code -number boolean [N] Number the sequences -width integer [60] Width of sequence to display (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] Offset to start numbering the sequence from (Any integer value) -html boolean [N] Use HTML formatting Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each 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 showseq 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 display in uppercase by giving the '-uppercase' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-upper @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 You can specify a file of ranges to highlight in a different colour when outputting in HTML format (using the '-html' qualifier) by giving the '-highlight' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-highlight @myfile'). The format of this file is very similar to the format of the above uppercase range file, except that the text after the start and end positions is used as the HTML colour name. This colour name is used 'as is' when specifying the colour in HTML in a '' construct, (where 'xxx' is the name of the colour). The standard names of HTML font colours are given in http://http://www.w3.org/TR/REC-html40/types.html#h-6.5 An example highlight range file is: # this is my set of ranges 12 23 red 4 5 darkturquoise 67 10348 #FFE4E1 You can specify a file of ranges to annotate by giving the '-annotate' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-annotate @myfile'). The format of this file is very similar to the format of the above highlight range file, except that the text after the start and end positions is used as the displayed text of the annotated region. An example annotation range file is: # this is my set of ranges 12 23 exon 1 4 5 CAP site 67 10348 exon 2 You can specify a file of enzyme names to read in by giving the '-enzymes' qualifier the name of the file holding the enzyme names with a '@' character in front of it, for example, '@enz.list'. Blank lines and lines starting with a '#' or '!' character are ignored and all other lines are concatenated together with a comma character ',' and then treated as the list of enzymes to search for. An example of a file of enzyme names is: # my enzymes HincII, ppiI # other enzymes hindiii HinfI Output file format Output files for usage example File: x13776.showseq X13776 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----| ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat |===============| promoter note="proposed rpoN-dependent promoter" | misc_feature note="last base of an XhoI site" 70 80 90 100 ----:----|----:----|----:----|----:----| ctacctggcgagcctggagcacgagcgggttcgcttcgta |===============| promoter note="proposed rpoN-dependent promoter" Output files for usage example 2 File: x13776.showseq X13776 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat ----:----|----:----|----:----|----:----|----:----|----:----| ccatggcgaccggctcgtagacgagctagtggtggtcggcccgctgcccttgacgtgcta ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac ----:----|----:----|----:----|----:----|----:----|----:----| gatggaccgctcggacctcgtgctcgcccaagcgaagcatgccgcgactcgctgtcagtg Output files for usage example 3 File: x13776.showseq ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat ctacctggcgagcctggagcacgagcgggttcgcttcgta Output files for usage example 4 File: x13776.showseq X13776 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 1 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat 60 61 ctacctggcgagcctggagcacgagcgggttcgcttcgta 100 Output files for usage example 5 File: x13776.showseq X13776 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 123 ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat 182 183 ctacctggcgagcctggagcacgagcgggttcgcttcgta 222 Output files for usage example 6 File: x13776.showseq X13776 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation ggtaccgCTGGCCGAGCATCTGCTcgatcaccaccagccgggcgacgggaactgcacgat ctacCTGGCGAGCCTGGAGCAcgagcgggttcgcttcgta Output files for usage example 7 File: x13776.showseq X13776 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----| ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat R S P P A G R R V |===============| promoter note="proposed rpoN-dependent promoter" | misc_feature note="last base of an XhoI site" 70 80 90 100 110 120 ----:----|----:----|----:----|----:----|----:----|----:----| ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac A S L |===============| promoter note="proposed rpoN-dependent promoter" Output files for usage example 8 File: x13776.showseq X13776 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----| ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat |------------| binding site | SNP |===============| promoter note="proposed rpoN-dependent promoter" | misc_feature note="last base of an XhoI site" 70 80 90 100 110 120 ----:----|----:----|----:----|----:----|----:----|----:----| ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac |===============| promoter note="proposed rpoN-dependent promoter" Most of the variants of the output format have already been described in the 'Description' and 'Usage' sections, but here is some more just to fill out this section ;-) The output format is extremely variable and under the control of the qualifiers used. The sequence can be formatted for HTML display by using the '-html' qualifier. The top and tail html tags , etc. are not included as it is expected that the output of this program will be included in a more extensive HTML page and so these parts are left to the user to provide. The name of the sequence is displayed, followed by the description of the sequence. These can be turned off with the '-noname' and '-nodescription' qualifiers. Then the sequence is output, one line at a time. Any associated information to be displayed is also output above and below the sequence line, as specified by the '-format' and or '-things' qualifiers. (See the 'Description' section for detals). The margins around the sequence are specified by the use of the '-margin' qaulifier and any numbering of the sequence and its translations are placed in the margin. A display of the restriction enzyme cut sites can be selected via '-format 6' option or the '-format 0 -thing b,r,s,-r' style of options. The option '-format 7' will produce a formatted display of cut sites on the sequence, with the six-frame translation below it. The cut sites are indicated by a slash character '\' that points to the poition between the nucleotides where the cuts occur. Cuts by many enzymes at the same position are indicated by stacking the enzyme names on top of each other. At the end the section header 'Enzymes that cut' is displayed followed by a list of the enzymes that cut the specified sequence and the number of times that they cut. The '-flatreformat' qualifier changes the display to emphasise the recognition site of the restriction enzyme, which is indicated by a row of '=' characters. The cut site if pointed to by a '>' or '<' character and if the cut site is not within or imemdiately adjacent to the recognition site, they are linked by a row or '.' characters. The name of the enzyme is displayed above (or below when the reverse sense site if displayed) the recognition site. The name of the enzyme is also displayed above the cut site if this occurs on a different display line to the recognition site (i.e. if it wraps onto the next line of sequence). 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 ------------------------------------------------------------------------------ The EMBOSS REBASE restriction enzyme data files are stored in directory 'data/REBASE/*' under the EMBOSS installation directory. These files must first be set up using the program 'rebaseextract'. Running 'rebaseextract' may be the job of your system manager. The data files are stored in the REBASE directory of the standard EMBOSS data directory. The names are: * embossre.enz Cleavage information * embossre.ref Reference/methylation information * embossre.sup Supplier information The column information is described at the top of the data files The reported enzyme from any one group of isoschizomers (the prototype) is specified in the REBASE database and the information is held in the data file 'embossre.equ'. You may edit this file to set your own preferred prototype, if you wish. The format of the file "embossre.equ" is Enzyme-name Prototype-name i.e. two columns of enzyme names separated by a space. The first name of the pair of enzymes is the name that is not preferred and the second is the preferred (prototype) name. Notes One or more things may be selected for display from a menu (-things option). The order of specified characters (upper or lower case) determines the order in the output: s Sequence b Blank line 1 Frame 1 translation 2 Frame 2 translation 3 Frame 3 translation -1 Frame -1 translation -2 Frame -2 translation -2 Frame -3 translation t Ticks line n Number ticks line c Complement sequence f Features (from the feature table or from a command line -ufo file) r Restriction enzyme cut sites in the forward sense -r Restriction enzyme cut sites in the reverse sense a User Annotation Alternatively, there is a selection of pre-defined formats to choose from. The codes from above used in the list of standard formats are: Sequence only: S A Default sequence: B N T S A F Pretty sequence: B N T S A One frame translation: B N T S B 1 A F Three frame translations: B N T S B 1 2 3 A F Six frame translations: B N T S B 1 2 3 T -3 -2 -1 A F Restriction enzyme map: B R S N T C -R B 1 2 3 T -3 -2 -1 A Baroque: B 1 2 3 N T R S T C -R T -3 -2 -1 A F The default standard format displays the following: for every new line that the sequence starts to write, the output display will contain first a blank line (b), then the position numbers of the ticks (n) then the ticks every 10 characters (t) then the sequence itself (s) then any user-supplied annotation (a) then the features from the feature table (f). Subsequent lines of the sequence output will repeat this format. The sequence can be translated, using the specified genetic code tables. The translation can be done in one, three or six frames. The translation can be displayed in one-letter or three-letter amino acid codes. The translation can optionally be displayed only when it is in open reading frames (ORFs) of a specified minimum size. One or more specified regions of the sequence can be individually translated. The output can be formatted for HTML. If the output is being formatted for HTML, then specified regions of the sequence can be displayed in any valid HTML colours. This program can use REBASE data to find the recognition sites and/or cut sites of restriction enzymes in a nucleic acid sequence. This program can display the cut sites on both strands. The -flatreformat option displays not only the cut sites which many other restriction cut-site programs will show, but also shows the recognition site. The Restriction Enzyme database (REBASE) is a collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Most recently, putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. The home page of REBASE is: http://rebase.neb.com/ If the sequence is in EMBL, Genbank or SwissProt format, the feature table of the sequence can be displayed with the sequence. GFF file features can also be displayed if they are included on the command line using -ufo=file. Other display options include: The displayed sequence can be numbered either by numbering the start and ending positions, or by placing a ruler with ticks above or below the sequence. An initial position to start the numbering from can be set. The width of a line, and width of a margin around the sequence reserved for numbering can be set. Specified regions of the sequence can be displayed in uppercase to highlight them. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None known. 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 plotorf Plot potential open reading frames in a nucleotide sequence prettyseq Write a nucleotide sequence and its translation to file recoder Find restriction sites to remove (mutate) with no translation change redata Retrieve information from REBASE restriction enzyme database remap Display restriction enzyme binding sites in a nucleotide sequence restover Find restriction enzymes producing a specific overhang restrict Report restriction enzyme cleavage sites in a nucleotide sequence showorf Display a nucleotide sequence and translation in pretty format silent Find restriction sites to insert (mutate) with no translation change sixpack Display a DNA sequence with 6-frame translation and ORFs transeq Translate nucleic acid sequences Author(s) Gary Williams formerly at: MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, 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 - GWW 23 Aug 2000 - features display added - GWW 20 Nov 2001 - feature matches and annotation display added - GWW 16 Dec 2008 - limited to nucleotide only. Use showpep for proteins - PMR Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None