showpep 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 protein sequences with features in pretty format Description showpep displays one or more protein 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. 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 showpep % showpep tsw:laci_ecoli -sbeg 1 -send 100 Displays protein 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:Baroque Display format [2]: Output file [laci_ecoli.showpep]: 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,t,s', we will output the sequence in the following way: % showpep tsw:laci_ecoli -sbeg 1 -send 120 Displays protein 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:Baroque Display format [2]: 0 Specify your own things to display S : Sequence B : Blank line T : Ticks line N : Number ticks line F : Features A : Annotation Enter a list of things to display [B,N,T,S,A,F]: b,t,s Output file [laci_ecoli.showpep]: Go to the output files for this example Example 3 Display only the sequence: % showpep tsw:laci_ecoli -sbeg 1 -send 100 -noname -nodesc -format 0 -thing S Displays protein sequences with features in pretty format Output file [laci_ecoli.showpep]: Go to the output files for this example Example 4 Protein sequence can be displayed in three-letter codes. (The codes are displayed downwards, so the first code is 'Met'): % showpep tsw:rs24_takru -three -format 2 Displays protein sequences with features in pretty format Output file [rs24_takru.showpep]: Go to the input files for this example Go to the output files for this example Example 5 Number the sequence lines in the margin: % showpep tsw:laci_ecoli -sbeg 1 -send 100 -format 1 -number Displays protein sequences with features in pretty format Output file [laci_ecoli.showpep]: Go to the output files for this example Example 6 Start the numbering at a specified value ('123' in this case): % showpep tsw:laci_ecoli -sbeg 1 -send 100 -format 1 -number -offset 123 Displays protein sequences with features in pretty format Output file [laci_ecoli.showpep]: Go to the output files for this example Example 7 Make selected regions uppercase. (Use '-slower' to force the rest of the sequence to be lowercase). % showpep tsw:laci_ecoli -sbeg 1 -send 100 -format 1 -slower -upper "17-17,22-22 " Displays protein sequences with features in pretty format Output file [laci_ecoli.showpep]: Go to the output files for this example Example 8 Add your own annotation to the display: % showpep tsw:laci_ecoli -sbeg 1 -send 100 -format 2 -send 120 -annotation "6-25 binding site 17-17 SNP 22-22 SNP" Displays protein sequences with features in pretty format Output file [laci_ecoli.showpep]: Go to the output files for this example Command line arguments Displays protein sequences with features in pretty format Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers (* if not always prompted): [-sequence] seqall (Gapped) protein 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: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, ticks line, blank line; then you should enter 'S,T,B'. (Values: S (Sequence); B (Blank line); T (Ticks line); N (Number ticks line); F (Features); A (Annotation)) [-outfile] outfile [*.showpep] Output file name Additional (Optional) qualifiers: -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'. -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) -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. 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. 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: -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 showpep reads one or more protein 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 'tsw:laci_ecoli' is a sequence entry in the example protein database 'tsw' Database entry: tsw:laci_ecoli ID LACI_ECOLI Reviewed; 360 AA. AC P03023; O09196; P71309; Q2MC79; Q47338; DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot. DT 19-JUL-2003, sequence version 3. DT 15-JUN-2010, entry version 117. DE RecName: Full=Lactose operon repressor; GN Name=lacI; OrderedLocusNames=b0345, JW0336; OS Escherichia coli (strain K12). OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; OC Enterobacteriaceae; Escherichia. OX NCBI_TaxID=83333; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX MEDLINE=78246991; PubMed=355891; DOI=10.1038/274765a0; RA Farabaugh P.J.; RT "Sequence of the lacI gene."; RL Nature 274:765-769(1978). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Chen J., Matthews K.K.S.M.; RL Submitted (MAY-1991) to the EMBL/GenBank/DDBJ databases. RN [3] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Marsh S.; RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases. RN [4] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / MG1655 / ATCC 47076; RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.; RT "Sequence of minutes 4-25 of Escherichia coli."; RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases. RN [5] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / MG1655 / ATCC 47076; RX MEDLINE=97426617; PubMed=9278503; DOI=10.1126/science.277.5331.1453; RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., RA Mau B., Shao Y.; RT "The complete genome sequence of Escherichia coli K-12."; RL Science 277:1453-1474(1997). RN [6] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911; RX PubMed=16738553; DOI=10.1038/msb4100049; RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.; RT "Highly accurate genome sequences of Escherichia coli K-12 strains [Part of this file has been deleted for brevity] FT CHAIN 1 360 Lactose operon repressor. FT /FTId=PRO_0000107963. FT DOMAIN 1 58 HTH lacI-type. FT DNA_BIND 6 25 H-T-H motif. FT VARIANT 282 282 Y -> D (in T41 mutant). FT MUTAGEN 17 17 Y->H: Broadening of specificity. FT MUTAGEN 22 22 R->N: Recognizes an operator variant. FT CONFLICT 286 286 L -> S (in Ref. 1, 4 and 7). FT HELIX 6 11 FT TURN 12 14 FT HELIX 17 24 FT HELIX 33 45 FT HELIX 51 56 FT STRAND 63 69 FT HELIX 74 89 FT STRAND 93 98 FT STRAND 101 103 FT HELIX 104 115 FT TURN 116 118 FT STRAND 122 126 FT HELIX 130 139 FT TURN 140 142 FT STRAND 145 150 FT STRAND 154 156 FT STRAND 158 161 FT HELIX 163 177 FT STRAND 181 186 FT HELIX 192 207 FT STRAND 213 217 FT HELIX 222 234 FT STRAND 240 246 FT HELIX 247 259 FT TURN 265 267 FT STRAND 268 271 FT HELIX 277 281 FT STRAND 282 284 FT STRAND 287 290 FT HELIX 293 308 FT STRAND 314 319 FT STRAND 322 324 FT STRAND 334 338 FT HELIX 343 353 FT HELIX 354 356 SQ SEQUENCE 360 AA; 38590 MW; 347A8DEE92D736CB CRC64; MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RVAQQLAGKQ SLLIGVATSS LALHAPSQIV AAIKSRADQL GASVVVSMVE RSGVEACKAA VHNLLAQRVS GLIINYPLDD QDAIAVEAAC TNVPALFLDV SDQTPINSII FSHEDGTRLG VEHLVALGHQ QIALLAGPLS SVSARLRLAG WHKYLTRNQI QPIAEREGDW SAMSGFQQTM QMLNEGIVPT AMLVANDQMA LGAMRAITES GLRVGADISV VGYDDTEDSS CYIPPLTTIK QDFRLLGQTS VDRLLQLSQG QAVKGNQLLP VSLVKRKTTL APNTQTASPR ALADSLMQLA RQVSRLESGQ // Input files for usage example 4 Database entry: tsw:rs24_takru ID RS24_TAKRU Reviewed; 132 AA. AC O42387; DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot. DT 01-JAN-1998, sequence version 1. DT 02-MAR-2010, entry version 42. DE RecName: Full=40S ribosomal protein S24; GN Name=rps24; OS Takifugu rubripes (Japanese pufferfish) (Fugu rubripes). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; OC Acanthomorpha; Acanthopterygii; Percomorpha; Tetraodontiformes; OC Tetradontoidea; Tetraodontidae; Takifugu. OX NCBI_TaxID=31033; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Crosio C., Cecconi F., Giorgi M., Amaldi F., Mariottini P.; RL Submitted (SEP-1997) to the EMBL/GenBank/DDBJ databases. CC -!- SIMILARITY: Belongs to the ribosomal protein S24e family. CC ----------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution-NoDerivs License CC ----------------------------------------------------------------------- DR EMBL; AJ001398; CAA04728.1; -; Genomic_DNA. DR SMR; O42387; 4-96. DR STRING; O42387; -. DR PRIDE; O42387; -. DR Ensembl; ENSTRUT00000016709; ENSTRUP00000016637; ENSTRUG00000006773; Takifu gu rubripes. DR eggNOG; fiNOG15754; -. DR InParanoid; O42387; -. DR GO; GO:0005840; C:ribosome; IEA:UniProtKB-KW. DR GO; GO:0000166; F:nucleotide binding; IEA:InterPro. DR GO; GO:0003735; F:structural constituent of ribosome; IEA:InterPro. DR GO; GO:0006412; P:translation; IEA:InterPro. DR InterPro; IPR012677; a_b_plait_nuc_bd. DR InterPro; IPR001976; Ribosomal_S24e. DR InterPro; IPR018098; Ribosomal_S24e_CS. DR Gene3D; G3DSA:3.30.70.330; a_b_plait_nuc_bd; 1. DR PANTHER; PTHR10496; Ribosomal_S24E; 1. DR Pfam; PF01282; Ribosomal_S24e; 1. DR ProDom; PD006052; Ribosomal_S24e; 1. DR PROSITE; PS00529; RIBOSOMAL_S24E; 1. PE 3: Inferred from homology; KW Ribonucleoprotein; Ribosomal protein. FT CHAIN 1 132 40S ribosomal protein S24. FT /FTId=PRO_0000137627. SQ SEQUENCE 132 AA; 15305 MW; DC437F60F20C14F5 CRC64; MNDTVTVRTR KFMTNRLLQR KQMVVDVLHP GKATVPKTEI REKLAKMYKT TPDVVFVFGF RTQFGGGKTT GFAMVYDSLD YAKKNEPKHR LARHGLFEKK KTSRKQRKER KNRMKKVRGT KKASVGASKK KD // 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 Output file format Output files for usage example File: laci_ecoli.showpep LACI_ECOLI Lactose operon repressor 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----| MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ |=========================================================== mature_protein_region note="Lactose operon repressor" ftid="PRO_00001 |========================================================| polypeptide_domain note="HTH lacI-type" |==================| |====| DNA_contact note="H-T-H motif" alpha_helix | mutated_variant_site note="Y->H: Broadening of specificity" | mutated_variant_site note="R->N: Recognizes an operator variant" |====| |===========| alpha_helix alpha_helix |=| turn |======| alpha_helix 70 80 90 100 ----:----|----:----|----:----|----:----| SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE ======================================== mature_protein_region note="Lactose operon repressor" ftid="PRO_00001 |=====| |====| beta_strand beta_strand |==============| alpha_helix Output files for usage example 2 File: laci_ecoli.showpep LACI_ECOLI Lactose operon repressor ----:----|----:----|----:----|----:----|----:----|----:----| MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ ----:----|----:----|----:----|----:----|----:----|----:----| SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVS Output files for usage example 3 File: laci_ecoli.showpep MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE Output files for usage example 4 File: rs24_takru.showpep RS24_TAKRU 40S ribosomal protein S24 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----| MAATVTVATALPMTAALLGALGMVVAVLHPGLATVPLTGIAGLLALMTLTTPAVVPVPGP esshaharhryhehsreelryleaasaeirlylharyhllrlyelyeyyhhrsaahahlh tnprlrlgrgsetrnguungsntllplusoysarlosruegusuastrsrroplleleye |=========================================================== mature_protein_region note="40S ribosomal protein S24" ftid="PRO_0000 70 80 90 100 110 120 ----:----|----:----|----:----|----:----|----:----|----:----| ATGPGGGLTTGPAMVTASLATALLAGPLHALAAHGLPGLLLTSALGALGALAAMLLVAGT rhlhlllyhhlhleayseesylyyslryirelrilehlyyyherylrylrysreyyarlh grneyyysrryeatlrpruprassnuossguagsyueusssrrgsngsugsngtsslgyr ============================================================ mature_protein_region note="40S ribosomal protein S24" ftid="PRO_0000 130 ----:----|-- LLASVGASLLLA yylealleyyys ssarlyarsssp ===========| mature_protein_region note="40S ribosomal protein S24" ftid="PRO_0000 Output files for usage example 5 File: laci_ecoli.showpep LACI_ECOLI Lactose operon repressor 1 MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ 60 61 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE 100 Output files for usage example 6 File: laci_ecoli.showpep LACI_ECOLI Lactose operon repressor 123 MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ 182 183 SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVE 222 Output files for usage example 7 File: laci_ecoli.showpep LACI_ECOLI Lactose operon repressor mkpvtlydvaeyagvsYqtvsRvvnqashvsaktrekveaamaelnyipnrvaqqlagkq slligvatsslalhapsqivaaiksradqlgasvvvsmve Output files for usage example 8 File: laci_ecoli.showpep LACI_ECOLI Lactose operon repressor 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----| MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQ |------------------| binding site | | SNP SNP |=========================================================== mature_protein_region note="Lactose operon repressor" ftid="PRO_00001 |========================================================| polypeptide_domain note="HTH lacI-type" |==================| |====| DNA_contact note="H-T-H motif" alpha_helix | mutated_variant_site note="Y->H: Broadening of specificity" | mutated_variant_site note="R->N: Recognizes an operator variant" |====| |===========| alpha_helix alpha_helix |=| turn |======| alpha_helix 70 80 90 100 110 120 ----:----|----:----|----:----|----:----|----:----|----:----| SLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVS ============================================================ mature_protein_region note="Lactose operon repressor" ftid="PRO_00001 |=====| |====| |=| beta_strand beta_strand turn |==============| |=| alpha_helix beta_strand |==========| alpha_helix 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. 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 t Ticks line n Number ticks line f Features (from the feature table or from a command line -ufo file) 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 Baroque: B N T S T 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 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. If the sequence is in 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 abiview Display the trace in an ABI sequencer file cirdna Draws circular maps of DNA constructs 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 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 sixpack Display a DNA sequence with 6-frame translation and ORFs 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 Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None