polydot 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 dotplots for all-against-all comparison of a sequence set Description polydot generates a dotplot for each of an all-against-all comparison of a set of sequences. The dotplots are rendered on a single diagram. The dotplot is an intuitive graphical representation of the regions of similarity between two sequences. All positions from the first input sequence are compared with all positions from the second input sequence searching for exact matches between sequence regions ("words"). The two sequences are the axes of the rectangular dotplot. Wherever there is "similarity" between a word from each sequences a dot is plotted. The wordsize is specified by the user. Optionally, information on the sequence and location of all the exact matching regions may be written to file as a feature file. Algorithm All sequence words of the specified size from the first input sequence are compared with all words from the second input sequence and exact matches identified. A line is plotted on the dotplot corresponding to any exact matching words. Thus any local regions of identity correspond to diagonals in the dotplot. Usage Here is a sample session with polydot % polydot globins.fasta -gtitle="Polydot of globins.fasta" -graph cps Draw dotplots for all-against-all comparison of a sequence set Word size [6]: Created polydot.ps Go to the input files for this example Go to the output files for this example Command line arguments Draw dotplots for all-against-all comparison of a sequence set Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers (* if not always prompted): [-sequences] seqset File containing a sequence alignment -wordsize integer [6] Word size (Integer 2 or more) * -outfeat featout [unknown.gff] Output features UFO -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: -[no]boxit boolean [Y] Draw a box around each dotplot -dumpfeat toggle [N] Dump all matches as feature files Advanced (Unprompted) qualifiers: -gap integer [10] This specifies the size of the gap that is used to separate the individual dotplots in the display. The size is measured in residues, as displayed in the output. (Integer 0 or more) 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 "-outfeat" associated qualifiers -offormat string Output feature format -ofopenfile string Features file name -ofextension string File name extension -ofdirectory string Output directory -ofname string Base file name -ofsingle boolean Separate file for each entry "-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 polydot reads in a set of nucleic or protein sequences. The sequences may or may not be aligned. Input files for usage example File: globins.fasta >HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK EFTPPVQAAYQKVVAGVANALAHKYH >HBB_HORSE Sw:Hbb_Horse => HBB_HORSE VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK DFTPELQASYQKVVAGVANALAHKYH >HBA_HUMAN Sw:Hba_Human => HBA_HUMAN VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA VHASLDKFLASVSTVLTSKYR >HBA_HORSE Sw:Hba_Horse => HBA_HORSE VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA VHASLDKFLSSVSTVLTSKYR >MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP GDFGADAQGAMNKALELFRKDIAAKYKELGYQG >GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA AVIADTVAAGDAGFEKLMSMICILLRSAY >LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSEVPQNNPEL QAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGVADAHFPVVKEAILKTIKE VVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA Output file format A graphical image is displayed on the specified graphics device. Output files for usage example Graphics File: polydot.ps [polydot results] Data files None. Notes Where the two sequences have substantial regions of identity, longer diagonal lines appear in the plot. It is possible to see at a glance such local regions of identity. It is also easy to see other features such as repeats (which form parallel diagonal lines), and insertions or deletions (which form breaks or discontinuities in the diagonal lines). References None. Warnings None. Diagnostic Error Messages None. Exit status 0 if successful. Known bugs None. See also Program name Description dotmatcher Draw a threshold dotplot of two sequences dotpath Draw a non-overlapping wordmatch dotplot of two sequences dottup Displays a wordmatch dotplot of two sequences 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. History Completed 2nd June 1999. Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None