prettyplot 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 Draw a sequence alignment with pretty formatting Description prettyplot draws a plot of the input sequence alignment. The sequences are rendered in pretty formatting on the specified graphics device. Drawing options control the appearance of the image, such as boxes, colour and shading for highlighting conserved regions. Usage Here is a sample session with prettyplot % prettyplot -resbreak=10 -boxcol -consensus -plurality=3 Draw a sequence alignment with pretty formatting Input (aligned) sequence set: globins.msf Graph type [x11]: cps Created prettyplot.ps Go to the input files for this example Go to the output files for this example Example 2 % prettyplot globins.msf -plurality=3 -docolour Draw a sequence alignment with pretty formatting Graph type [x11]: cps Created prettyplot.ps Go to the output files for this example Command line arguments Draw a sequence alignment with pretty formatting Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequences] seqset (Aligned) sequence set filename and optional format, or reference (input USA) -graph graph [$EMBOSS_GRAPHICS value, or x11] Graph type (ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg) Additional (Optional) qualifiers: -matrixfile matrix [EBLOSUM62 for protein, EDNAFULL for DNA] This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. -residuesperline integer [50] The number of residues to be displayed on each line (Any integer value) -resbreak integer [Same as -residuesperline to give no breaks] Residues before a space (Integer 1 or more) -[no]ccolours boolean [Y] Colour residues by their consensus value. -cidentity string [RED] Colour to display identical residues (RED) (Any string) -csimilarity string [GREEN] Colour to display similar residues (GREEN) (Any string) -cother string [BLACK] Colour to display other residues (BLACK) (Any string) -docolour boolean [N] Colour residues by table oily, amide etc. -shade string Set to BPLW for normal shading (black, pale, light, white) so for pair = 1.5,1.0,0.5 and shade = BPLW Residues score Colour 1.5 or over... BLACK (B) 1.0 to 1.5 ... BROWN (P) 0.5 to 1.0 ... WHEAT (L) under 0.5 .... WHITE (W) The only four letters allowed are BPLW, in any order. (Any string up to 4 characters, matching regular expression /^([BPLW]{4})?$/) -pair array [1.5,1.0,0.5] Values to represent identical similar related -identity integer [0] Only match those which are identical in all sequences. (Integer 0 or more) -[no]box boolean [Y] Display prettyboxes -boxcol boolean [N] Colour the background in the boxes -boxuse string [GREY] Colour to be used for background. (GREY) (Any string) -[no]name boolean [Y] Display the sequence names -maxnamelen integer [10] Margin size for the sequence name. (Any integer value) -[no]number boolean [Y] Display the residue number -[no]listoptions boolean [Y] Display the date and options used -plurality float [Half the total sequence weighting] Plurality check value (totweight/2) (Any numeric value) -consensus boolean [N] Display the consensus -[no]collision boolean [Y] Allow collisions in calculating consensus -alternative menu [0] Values are 0:Normal collision check. (default) 1:Compares identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred. 2:If another residue has a greater than or equal to matching score and these do not match then a collision has occurred. 3:Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured. (Values: 0 (Normal collision check. (default)); 1 (Compares identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred.); 2 (If another residue has a greater than or equal to matching score and these do not match then a collision has occurred.); 3 (Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured.)) -showscore integer [-1] Print residue scores (Any integer value) -portrait boolean [N] Set page to Portrait Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequences" 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 "-graph" associated qualifiers -gprompt boolean Graph prompting -gdesc string Graph description -gtitle string Graph title -gsubtitle string Graph subtitle -gxtitle string Graph x axis title -gytitle string Graph y axis title -goutfile string Output file for non interactive displays -gdirectory 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 prettyplot reads aligned 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 File: globins.msf !!AA_MULTIPLE_ALIGNMENT 1.0 ../data/globins.msf MSF: 164 Type: P 25/06/01 CompCheck: 4278 .. Name: HBB_HUMAN Len: 164 Check: 6914 Weight: 0.61 Name: HBB_HORSE Len: 164 Check: 6007 Weight: 0.65 Name: HBA_HUMAN Len: 164 Check: 3921 Weight: 0.65 Name: HBA_HORSE Len: 164 Check: 4770 Weight: 0.83 Name: MYG_PHYCA Len: 164 Check: 7930 Weight: 1.00 Name: GLB5_PETMA Len: 164 Check: 1857 Weight: 0.91 Name: LGB2_LUPLU Len: 164 Check: 2879 Weight: 0.43 // 1 50 HBB_HUMAN ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR HBB_HORSE ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR HBA_HUMAN ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS HBA_HORSE ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG MYG_PHYCA ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD 51 100 HBB_HUMAN FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE HBB_HORSE FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE HBA_HUMAN FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD HBA_HORSE FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD MYG_PHYCA KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN 101 150 HBB_HUMAN LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA HBB_HORSE LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA HBA_HUMAN LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS HBA_HORSE LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS MYG_PHYCA SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA 151 164 HBB_HUMAN NALAHKYH~~~~~~ HBB_HORSE NALAHKYH~~~~~~ HBA_HUMAN TVLTSKYR~~~~~~ HBA_HORSE TVLTSKYR~~~~~~ MYG_PHYCA KDIAAKYKELGYQG GLB5_PETMA Y~~~~~~~~~~~~~ LGB2_LUPLU IVIKKEMNDAA~~~ Output file format The output is to the specified graphics device. The results can be output in one of several formats by using the command-line qualifier -graph xxx, where 'xxx' is replaced by the name of the required device. Support depends on the availability of third-party software packages. The device names that output to a file are: ps (postscript), cps (colourps), png, gif, pdf, svg, hpgl, hp7470, hp7580, das, data. The other available device names are: meta, x11 (xwindows), tek (tek4107t), tekt (tektronix), xterm, text. Output can be turned off by specifying none (null). See: http://emboss.sf.net/docs/themes/GraphicsDevices.html for further information on supported devices. Output files for usage example Graphics File: prettyplot.ps [prettyplot results] Output files for usage example 2 Graphics File: prettyplot.ps [prettyplot results] Data files Prettyplot uses a comparison matrix file to calculate similarity to the consensus. For protein sequences EBLOSUM62 is used for the substitution matrix. For nucleotide sequence, EDNAFULL is used. 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 A consesnsus sequence is calculated for the alignment and individual sequences compared to the consensus using the specified comparison matrix file. The default matrix for protein sequences is EBLOSUM62 and for nucleotide sequences is EDNAFULL. The drawing options render conserved sites and regions identified from the comparisons. For example, residues in a sequence are classed as "identical", "similar" or "other" to the consensus depending on user-specified thresholds of sequence similarity (-pair option). Residues in each class are rendered red, green and black by default (this can be changed). There are other more general drawing options, for example, controlling the number of residues displayed per line, background shading and whether to display sequence names or not. References None. Warnings None. Diagnostic Error Messages None. Exit status It exits with status 0 unless an error is reported. Known bugs Portrait mode does not cover the whole page! This is a "feature" in plplot. See also Program name Description abiview Display the trace in an ABI sequencer file cirdna Draws circular maps of DNA constructs edialign Local multiple alignment of sequences emma Multiple sequence alignment (ClustalW wrapper) iep Calculate the isoelectric point of proteins infoalign Display basic information about a multiple sequence alignment 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 plotcon Plot conservation of a sequence alignment plotorf Plot potential open reading frames in a nucleotide sequence prettyseq Write a nucleotide sequence and its translation to file remap Display restriction enzyme binding sites in a nucleotide sequence showalign Display a multiple sequence alignment in pretty format showfeat Display features of a sequence in pretty format showpep Displays protein sequences with features in pretty format sixpack Display a DNA sequence with 6-frame translation and ORFs tranalign Generate an alignment of nucleic coding regions from aligned proteins Author(s) Ian Longden formerly at: Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. Many features were first implemented in the EGCG program "prettyplot" by Peter Rice 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. The original suggestions for the PrettyPlot program were from Denis Duboule and Sigfried Labeit at EMBL. Gert Vriend added the star marking. Rita Grandori suggested the -NOCOLLISION option. History Completed 5th May 1999. Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None