dotpath 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 non-overlapping wordmatch dotplot of two sequences Description dotpath generates a dotplot from two input sequences. The dotplot is an intuitive graphical representation of the regions of similarity between two sequences. Sequence "words" of a user-specified length are compared and all exact word matches between the two sequences are recorded. The set of the longest possible but non-overlapping matches is identified. The two sequences are the axes of the rectangular dotplot. Wherever there is an exact matching word in the two sequences a line is plotted. Algorithm dotpath uses the same algorithm as diffseq and dottup for finding a minimal set of exact matches between two sequences. It finds all identical words of size -wordsize or greater in the two sequences. It then reduces the matches found to the minimal set of matches that do not overlap. This set is rendered as lines in the dotplot. Usage Here is a sample session with dotpath % dotpath tembl:AF129756 tembl:BA000025 -word 20 -graph cps -overlaps Draw a non-overlapping wordmatch dotplot of two sequences Created dotpath.ps Go to the input files for this example Go to the output files for this example Command line arguments Draw a non-overlapping wordmatch dotplot of two sequences Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-asequence] sequence Sequence filename and optional format, or reference (input USA) [-bsequence] sequence Sequence filename and optional format, or reference (input USA) -wordsize integer [4] Word size (Integer 2 or more) -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: -overlaps boolean [N] Displays the overlapping matches (in red) as well as the minimal set of non-overlapping matches -[no]boxit boolean [Y] Draw a box around dotplot Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-asequence" associated qualifiers -sbegin1 integer Start of the sequence to be used -send1 integer End of the 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 "-bsequence" associated qualifiers -sbegin2 integer Start of the sequence to be used -send2 integer End of the sequence to be used -sreverse2 boolean Reverse (if DNA) -sask2 boolean Ask for begin/end/reverse -snucleotide2 boolean Sequence is nucleotide -sprotein2 boolean Sequence is protein -slower2 boolean Make lower case -supper2 boolean Make upper case -sformat2 string Input sequence format -sdbname2 string Database name -sid2 string Entryname -ufo2 string UFO features -fformat2 string Features format -fopenfile2 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 Input files for usage example 'tembl:AF129756' is a sequence entry in the example nucleic acid database 'tembl' Database entry: tembl:AF129756 ID AF129756; SV 1; linear; genomic DNA; STD; HUM; 184666 BP. XX AC AF129756; XX DT 12-MAR-1999 (Rel. 59, Created) DT 14-NOV-2006 (Rel. 89, Last updated, Version 5) XX DE Homo sapiens MSH55 gene, partial cds; and CLIC1, DDAH, G6b, G6c, G5b, G6d, DE G6e, G6f, BAT5, G5b, CSK2B, BAT4, G4, Apo M, BAT3, BAT2, AIF-1, 1C7, LST-1, DE LTB, TNF, and LTA genes, complete cds. XX KW . XX OS Homo sapiens (human) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; OC Homo. XX RN [1] RP 1-184666 RX DOI; 10.1101/gr.1736803. RX PUBMED; 14656967. RA Xie T., Rowen L., Aguado B., Ahearn M.E., Madan A., Qin S., Campbell R.D., RA Hood L.; RT "Analysis of the gene-dense major histocompatibility complex class III RT region and its comparison to mouse"; RL Genome Res. 13(12):2621-2636(2003). XX RN [2] RP 1-184666 RA Rowen L., Madan A., Qin S., Shaffer T., James R., Ratcliffe A., Abbasi N., RA Dickhoff R., Loretz C., Madan A., Dors M., Young J., Lasky S., Hood L.; RT "Sequence of the human major histocompatibility complex class III region"; RL Unpublished. XX RN [3] RP 1-184666 RA Rowen L.; RT ; RL Submitted (22-FEB-1999) to the EMBL/GenBank/DDBJ databases. RL Department of Molecular Biotechnology, Box 357730 University of Washington, RL Seattle, WA 98195, USA XX RN [4] RP 1-184666 RA Rowen L.; RT ; RL Submitted (28-OCT-1999) to the EMBL/GenBank/DDBJ databases. RL Multimegabase Sequencing Center, University of Washington, PO Box 357730, RL Seattle, WA 98195, USA [Part of this file has been deleted for brevity] aaaccagttt accaccactc ctaacactaa acttaaatct gactctaaat gtaagtccaa 181740 tctgagccac aagcctaaag ttgaacttta tcctgcttta tgaattattc atccattcct 181800 ccatttagtg agtatctgcg tgcctaacac atgctgggca ttgtcctaag gcaggaggga 181860 catggaggca aagggatcag agaaggtacc agcacctgtg gagcttgtat tccagtgagg 181920 ccagacggaa aagaaagaaa ctgaagaaga aattggtact atgagaaaat aagacaggct 181980 gatgttgtaa gagtggcagg gagctacttt taaatacagt agtcagcaaa atcctctttg 182040 agtgtttggg tggcactgga gctgagaccc aaatgacaaa aaatagtgac caggtaaaag 182100 tttgggagca aagcatttca ggtaaaggga gcagctactg caaaggctgg aaggcggaac 182160 caagctgggg gtgttgacga caaacagaag gccagtgtgg ctggagcaga gagagagact 182220 gggaggcggg tgggagatga ggtcagagag gagggcaggg gccaggtcat gcagggccat 182280 gcaagaaggg taaagcctct agatttcatc cagccacagg aagcctttaa aggtcgtcag 182340 agtgtgtggt gcgtgcgtgt gtgtgtgtgt gtgtgtgtgt gttgcagggg agagaggggg 182400 agggagagag agagagagag agagaagagg gaggtgagca gaggtgattg gatttttttt 182460 tcttttgaca tggtgtcttg ctctgtggcc taggctggag tgcagtggca ccatcatagc 182520 ccactgcaac ctcaaaacca tgggctcaag tcatccttcc acctcagctt cccaagtatc 182580 taggactaca ggtgtgtgcc actgtgcctg gctaatttta aaaaatattt taaaattttt 182640 gttgagacag ggtctatgct gctcaggctg gtctcgaact cctggtttca agtgatctgc 182700 ccatcttggc ctcccaaagt ttttttttgt tagtttgaga ggcggtttcg ctcgttgccc 182760 aggctggagt gcaatgactg atctcatctc actgcaacct ctgcctcctg ggttcaagcg 182820 attctcctgc ttcagcctcc caagtagctg ggattacagg tgcatgccac cattcccggc 182880 taattttttg tatttagtag agatggggtt tcaccatgtt agtcaggctg atctcaaact 182940 cctgacctca ggtgatccgc ctgcctcagc ctcccaaagt tttgggatta caggtgtgag 183000 ccaccatgct gggccagcct cccaaagttt tgggattaca ggcatgagtc accacactgg 183060 ccctggattt tttttctttc ttttttttgg agacggagtc tcactctgtt gcccaggctg 183120 gagtgcaatg gcgtaatctc agctcactgc aacctctgct gcccgggttc aaacgattct 183180 cctgtcttag cctcctgagt agctgggatt ataggtgcat gccaccatgc ctggctaatt 183240 tttgtacttt tagtagagaa agtacaccat cttggccagg ctggtctcga actcctgacc 183300 tcaggtgatc cacttgcgtc ggcctcccaa agtgctggga ttacaggcgt gagacaccgc 183360 acccagcctt tttttttttt tttcttttaa gacagaatcg ctctgtcacc caggctggag 183420 tgcagtggca caatctcggc tcactgcaac ctctgcctcc caggtttaag caatccacct 183480 atgtcagtct cccaagtagc tgggattata ggtgcatgtc accatgcctg gctaattttt 183540 gtacttttag tatagaaagt acaccatgtt ggccaggctg gtcttgaact cctgacctca 183600 agtgatccgc ctgcctcagc ctcccgaagt gctggaatta cagacatgtg ccactgcacc 183660 cggcctggtt ttttttttct aagagatgga gtctcacttt tctgcccagg ttggagtgca 183720 atggcaccat catagctcac tgcagccttc aactcttggc ctcaggcaat ccttgcacct 183780 tagcctcgca gtgttgggat tacaggcatg agccactgag ccttgcctgg actttttttt 183840 ttttttgaga tggcgtctcg ctctgttgcc caggttggag tgctacggca tgatcttggc 183900 tcactgcaac ttccacctcc caggttcaag cgattctctt gcctcggccc cccgagtagc 183960 tgggattaca ggcatgcgcc accgtgcctg gctaattttg gtatttttag tagagatagg 184020 gtttcatcat gttgggcagg ctggtcttga actcctgacc tcgtgatcca cccacctcgg 184080 cctcccaaag tgctgggatt ataggcatag ccaacgcgcc cagcctggac ttgtttttaa 184140 aagatcactg tggctcctgt gtttaggctg gctggtagga gacaggtggc agtggcattg 184200 atggtgaaga gaaaatagtg gcagccatgg agatggagag aagtagacaa gtttgggata 184260 tattatacat tccaggggta gaaacaacag gactagatga tggattgatg ggtgggagat 184320 gtagatactg ggagagaagc aggattctga tggatggaaa aactaaaaaa ttctattttg 184380 ggtgtggtaa gtctaagtct attagacatg caagtagaga tgtcactggg cagatacaca 184440 tctggatttc aggggcaagg tccaagctag agaaagaaac ctgggcatgg tcagcatgag 184500 gatggtgttt aaagccatgg aacttatctt gtgcatccct ataagacccc tttgaggcac 184560 ttgtttcccc tcacaatgga tgcagtgcat cttccattct gaattccaga ggcaacaacc 184620 tcctgctcct agaagctaaa ctctccagac ttagtcttct gaattc 184666 // Database entry: tembl:BA000025 ID BA000025; SV 2; linear; genomic DNA; STD; HUM; 2229817 BP. XX AC BA000025; AP000502-AP000521; XX DT 09-DEC-2004 (Rel. 82, Created) DT 17-JUN-2008 (Rel. 96, Last updated, Version 5) XX DE Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region. XX KW . XX OS Homo sapiens (human) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; OC Homo. XX RN [1] RP 1-2229817 RA Hirakawa M., Yamaguchi H., Imai K., Shimada J.; RT ; RL Submitted (21-AUG-2001) to the EMBL/GenBank/DDBJ databases. RL Mika Hirakawa, Japan Science and Technology Corporation (JST), Advanced RL Databases Department; 5-3, Yonbancho, Chiyoda-ku, Tokyo 102-0081, Japan RL (E-mail:mika@tokyo.jst.go.jp, URL:http://www-alis.tokyo.jst.go.jp/, RL Tel:81-3-5214-8491, Fax:81-3-5214-8470) XX RN [2] RA Shiina S., Tamiya G., Oka A., Inoko H.; RT "Homo sapiens 2,229,817bp genomic DNA of 6p21.3 HLA class I region"; RL Unpublished. XX DR EPD; EP11158; HS_TNF. DR EPD; EP11159; HS_LTA. DR EPD; EP73522; HS_HLA-B. DR EPD; EP73908; HS_GTF2H4. DR EPD; EP73940; HS_NEU1. DR EPD; EP74013; HS_VARS2. DR EPD; EP74203; HS_MRPS18B. DR EPD; EP74346; HS_HLA-E. DR EPD; EP74389; HS_BAT1. DR EPD; EP74485; HS_IER3. DR GDB; 11515913. DR GOA; P59942. DR HGNC; 20668; MCCD1. DR IMGT/HLA; HLA02629; J*01:01:01:02. DR IMGT/HLA; HLA02802; V*01:01:01:02. DR RFAM; RF00017; SRP_euk_arch. DR RFAM; RF00019; Y_RNA. DR RFAM; RF00026; U6. DR RFAM; RF00100; 7SK. [Part of this file has been deleted for brevity] ttggccccac cccagcatgt ctccaggttc ctctcagccc tggttccttt tggccctgca 2226900 gtcacaatgg gcaacactgt gacgcaccct gtcctgtgtc acagtgtcat acactcaggc 2226960 tcacattgcc cctaggccac ttgccagcca agggacatgg ccacattttg tgtcttctgc 2227020 acctcagcct tgctttcaag tgcaggtgat gatggcaccc acgcagaaca aatgttattt 2227080 gctatcttcg tcgagtttag tcatccaatt ttccaaccct cactgggcaa ggaagagtgt 2227140 ggtttccacc aagaaggcag gatgtcagca gtcacagggg caaccaacag ggaaagccgc 2227200 cggaaaatag accccacagg aagcacaggt gtccagtgga gatgggaacc ctgcagattt 2227260 gaccgtcttt aagcagatta gagagattac cgttactaac aacttagcca taaaagttta 2227320 ttagctattt tcaaaaagca taaaattatg taatataatt ttttttaaat ttccatcaat 2227380 acaaaactaa tctgggcact gcaacttccg gtgggcaact gggataggcg gcatcatcag 2227440 gaaggcgagc cctgccgtgc cccatgtgcc agtgccccag atggcggcag cctccccaga 2227500 agcaccttgt atctcccctg cacagggcca gggtcccagc ttcccataca ccttctcctg 2227560 ctttttcttt tctgtccttt cctttttcaa taaaccacct gcaaaaaggg aaaaccattc 2227620 tgaggacaag aaacatgtca atgggaaata cacagttgcc agagggtaaa aggccctgtt 2227680 cattctcatt gaaaagctca ggtatttctg ttaaagtctc tccttttact ttaggatgct 2227740 gactcctgcg tccatctcaa cctgggcatc gtgccaccac cttcaagaag agaaaaacta 2227800 agtagtgctt tgcaaagggg cagcagcatt tctcatttct gaccatgtca ggcacatggc 2227860 catgcagatg agcaggtggg ggacacaggt gagtctccag acctgctctc ctcccacagt 2227920 acattcttga gtctttttaa acagttgtga aaatgccaca gatgcaagca cctgtgggcc 2227980 actcccatgg ggaccgttgc acaaggcagt gccactcatt ctcagaacct cctaccatgg 2228040 gctatgctta gtgacccgag gccaagccaa ggaagacgcc agccacaggg tgccatcctc 2228100 aggggcatgc tgccagcagg ggcaaagtta tccctagcaa caagatacag aaagaaagaa 2228160 aaaaggaagg aaatgtagcc aatgggccgg ttcaggttct tgactttgcc acacaaaaga 2228220 atttgagagc aagtccaaag taaaagtcag caagagaatt tattgcaaag tgaaagtaca 2228280 ctctgacagc tgatcagagc agctgctcaa aagagagaca gtaccctccc ctcacgggag 2228340 tcttacatga ttattcatga ataggtggga aggggtattg ttttaagcat gttctgtggt 2228400 ctcttgaacg tgcatgcact gtggttgtac atatcagcac acacatctta cgtctcatta 2228460 gcatcttaac ttccctctca gagttgtgtt tgctactatt gtaatgagca taggtcagcc 2228520 caaggacact attcatgggt ttctgggctt cctcagatgt ggggatgcct cccttggctc 2228580 ttctacctct ttgctgcagg atgttctaac cacaagccca ggatatggtt tgcgcactgt 2228640 cgaacagctt gttctctcca tcaacctgac aagtctcttg tttcctttca agggaggctg 2228700 tgaacaccct atctcactga cctcagaagg acagtacagc agtagccacc atgaccaaaa 2228760 agatgattcc agaagtgcag gacaactccc tacccagagg ctgtggctgt gcagtaacac 2228820 accaagaggg gagtccagct ggctctcagg gtgctcacta ccctcatctg ggggcctgga 2228880 ggacgtcaat tcctgagaac gccacgttct agtgagtaga atgaactgag agatacacag 2228940 caaagctcca catacttttc cttttctttg tgcccgcagt gttcttcatc agtgtgctct 2229000 cgcttttcag ctactactgt tggctggctg gaaaaaatag aacaatagta aaaattagag 2229060 accagtcttt ggtgatgaag agaaatattg gctacttcca gtattttcta gctttggtta 2229120 tggttgcagt tttccagctc accttgtggg gatgaattca gaaaaaagtt acaaattgaa 2229180 atgaacatgc cagaagtatt ggctcaaatc aacgttgtcc tattaagcca cttagtgaat 2229240 caaaagaccg cttgttggac tgttaatctc ggtggccaga gaaaggagct gaagaaggtg 2229300 ttgccagatc aggaacaaat aattacagcg gcaatagaaa atggaagacc acttgttcat 2229360 aaccatttga ataagggcaa ggtgtatgga aacacattat gaactgatat tttcagtttt 2229420 gtttgcaaga aaatgattaa taaggtgaaa taattgaagt atcacggaag atacattaaa 2229480 aaaaaaaaaa gcctttgtac agtttgctgg agccacagat gtcctactcc agagcagaac 2229540 aatgcctgaa tcttcagggt ccatttctgc cgcattcact agcaaccaca aatgtgactt 2229600 aattttactt tggaaataat gcttacccat tgtgagatgc tgtaatatga accatcatta 2229660 catgttaaca tggcacatgg aattttgagt gtctaagtta catttttaga gttgtttctt 2229720 agtagccatg tgagtttcca ctccaaaaac acaagctaaa aacttgtttt gagtgaagga 2229780 catctagggc aaatggtggc tgaaagtgaa tgagatc 2229817 // Output file format In normal operation, a dotplot image is displayed. With the -data qualifier a file of the positions of the matches in the minimal non-overlapping set of matches is output. Output files for usage example Graphics File: dotpath.ps [dotpath results] Notes For similar sequences, dotpath provides a convenient way to find a path that aligns the two sequences well. It is not a true optimal path as produced by the dynamic programming algorithms used in water or needle, but for very closely related sequences it will produce the same result. In contast to full alignment, it works very quickly with very long sequences. The entire set of matches found can be displayed with the -overlaps qualifier. This shows all matches in red, except for those in the minimal path (non-overlapping set) which are shown in black, as normal. Using a longer word size will create a dottplot with relatively less noise; the matches are longer and therefore more likely to have biological meaning. Such runs will be much faster, but of course are less sensitive. References None Warnings If you give a small word size with a very large sequence you will run out of memory. If this happens, try again with a larger word size. Diagnostic Error Messages None Exit status It always exits with status 0. Known bugs None See also Program name Description dotmatcher Draw a threshold dotplot of two sequences dottup Displays a wordmatch dotplot of two sequences polydot Draw dotplots for all-against-all comparison of a sequence set This program is closely based on dottup with the addition of by default displaying only the minimal set of non-overlapping matches. This program uses the same algorithm as diffseq for finding a minimal set of very good matches between two sequences. diffseq may be more convenient if you are looking at the differences between two nearly identical 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 14 Aug 2000. Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None