polydot Function Displays all-against-all dotplots of a set of sequences Description A dotplot is a graphical representation of the regions of similarity between two sequences. The two sequences are placed on the axes of a rectangular image and (subject to threshold conditions) wherever there is a similarity between the sequences a dot is placed on the image. Where the two sequences have substantial regions of similarity, many dots align to form diagonal lines. It is therefore possible to see at a glance where there are local regions of similarity. polydot compares all sequences in a set of sequences, draws a dotplot for each pair of sequences by marking where words (tuples) of a specified length have an exact match in both sequences and optionally reports all identical matches to feature files. Usage Here is a sample session with polydot % polydot globins.fasta -gtitle="Polydot of globins.fasta" -graph cps Displays all-against-all dotplots of a set of sequences 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 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, tekt, tek, none, data, xterm, png, gif) 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 standard output -filter boolean Read standard input, write 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. 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 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 None. References None. Warnings None. Diagnostic Error Messages None. Exit status 0 if successful. Known bugs None. See also Program name Description dotmatcher Displays a thresholded dotplot of two sequences dotpath Non-overlapping wordmatch dotplot of two sequences dottup Displays a wordmatch dotplot of two sequences Author(s) Ian Longden (il © sanger.ac.uk) Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. 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