
                                  dotpath 



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

   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,
                                  tekt, tek, none, data, xterm, png, gif)

   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. 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

  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    18174
0
     tctgagccac aagcctaaag ttgaacttta tcctgcttta tgaattattc atccattcct    18180
0
     ccatttagtg agtatctgcg tgcctaacac atgctgggca ttgtcctaag gcaggaggga    18186
0
     catggaggca aagggatcag agaaggtacc agcacctgtg gagcttgtat tccagtgagg    18192
0
     ccagacggaa aagaaagaaa ctgaagaaga aattggtact atgagaaaat aagacaggct    18198
0
     gatgttgtaa gagtggcagg gagctacttt taaatacagt agtcagcaaa atcctctttg    18204
0
     agtgtttggg tggcactgga gctgagaccc aaatgacaaa aaatagtgac caggtaaaag    18210
0
     tttgggagca aagcatttca ggtaaaggga gcagctactg caaaggctgg aaggcggaac    18216
0
     caagctgggg gtgttgacga caaacagaag gccagtgtgg ctggagcaga gagagagact    18222
0
     gggaggcggg tgggagatga ggtcagagag gagggcaggg gccaggtcat gcagggccat    18228
0
     gcaagaaggg taaagcctct agatttcatc cagccacagg aagcctttaa aggtcgtcag    18234
0
     agtgtgtggt gcgtgcgtgt gtgtgtgtgt gtgtgtgtgt gttgcagggg agagaggggg    18240
0
     agggagagag agagagagag agagaagagg gaggtgagca gaggtgattg gatttttttt    18246
0
     tcttttgaca tggtgtcttg ctctgtggcc taggctggag tgcagtggca ccatcatagc    18252
0
     ccactgcaac ctcaaaacca tgggctcaag tcatccttcc acctcagctt cccaagtatc    18258
0
     taggactaca ggtgtgtgcc actgtgcctg gctaatttta aaaaatattt taaaattttt    18264
0
     gttgagacag ggtctatgct gctcaggctg gtctcgaact cctggtttca agtgatctgc    18270
0
     ccatcttggc ctcccaaagt ttttttttgt tagtttgaga ggcggtttcg ctcgttgccc    18276
0
     aggctggagt gcaatgactg atctcatctc actgcaacct ctgcctcctg ggttcaagcg    18282
0
     attctcctgc ttcagcctcc caagtagctg ggattacagg tgcatgccac cattcccggc    18288
0
     taattttttg tatttagtag agatggggtt tcaccatgtt agtcaggctg atctcaaact    18294
0
     cctgacctca ggtgatccgc ctgcctcagc ctcccaaagt tttgggatta caggtgtgag    18300
0
     ccaccatgct gggccagcct cccaaagttt tgggattaca ggcatgagtc accacactgg    18306
0
     ccctggattt tttttctttc ttttttttgg agacggagtc tcactctgtt gcccaggctg    18312
0
     gagtgcaatg gcgtaatctc agctcactgc aacctctgct gcccgggttc aaacgattct    18318
0
     cctgtcttag cctcctgagt agctgggatt ataggtgcat gccaccatgc ctggctaatt    18324
0
     tttgtacttt tagtagagaa agtacaccat cttggccagg ctggtctcga actcctgacc    18330
0
     tcaggtgatc cacttgcgtc ggcctcccaa agtgctggga ttacaggcgt gagacaccgc    18336
0
     acccagcctt tttttttttt tttcttttaa gacagaatcg ctctgtcacc caggctggag    18342
0
     tgcagtggca caatctcggc tcactgcaac ctctgcctcc caggtttaag caatccacct    18348
0
     atgtcagtct cccaagtagc tgggattata ggtgcatgtc accatgcctg gctaattttt    18354
0
     gtacttttag tatagaaagt acaccatgtt ggccaggctg gtcttgaact cctgacctca    18360
0
     agtgatccgc ctgcctcagc ctcccgaagt gctggaatta cagacatgtg ccactgcacc    18366
0
     cggcctggtt ttttttttct aagagatgga gtctcacttt tctgcccagg ttggagtgca    18372
0
     atggcaccat catagctcac tgcagccttc aactcttggc ctcaggcaat ccttgcacct    18378
0
     tagcctcgca gtgttgggat tacaggcatg agccactgag ccttgcctgg actttttttt    18384
0
     ttttttgaga tggcgtctcg ctctgttgcc caggttggag tgctacggca tgatcttggc    18390
0
     tcactgcaac ttccacctcc caggttcaag cgattctctt gcctcggccc cccgagtagc    18396
0
     tgggattaca ggcatgcgcc accgtgcctg gctaattttg gtatttttag tagagatagg    18402
0
     gtttcatcat gttgggcagg ctggtcttga actcctgacc tcgtgatcca cccacctcgg    18408
0
     cctcccaaag tgctgggatt ataggcatag ccaacgcgcc cagcctggac ttgtttttaa    18414
0
     aagatcactg tggctcctgt gtttaggctg gctggtagga gacaggtggc agtggcattg    18420
0
     atggtgaaga gaaaatagtg gcagccatgg agatggagag aagtagacaa gtttgggata    18426
0
     tattatacat tccaggggta gaaacaacag gactagatga tggattgatg ggtgggagat    18432
0
     gtagatactg ggagagaagc aggattctga tggatggaaa aactaaaaaa ttctattttg    18438
0
     ggtgtggtaa gtctaagtct attagacatg caagtagaga tgtcactggg cagatacaca    18444
0
     tctggatttc aggggcaagg tccaagctag agaaagaaac ctgggcatgg tcagcatgag    18450
0
     gatggtgttt aaagccatgg aacttatctt gtgcatccct ataagacccc tttgaggcac    18456
0
     ttgtttcccc tcacaatgga tgcagtgcat cttccattct gaattccaga ggcaacaacc    18462
0
     tcctgctcct agaagctaaa ctctccagac ttagtcttct gaattc                   18466
6
//

  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   14-NOV-2006 (Rel. 89, Last updated, Version 4)
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   IMGT/HLA; HLA02629; J*01010102.
DR   RFAM; RF00017.
DR   RFAM; RF00019.
DR   RFAM; RF00026.
DR   RFAM; RF00100.
DR   RFAM; RF00137.
DR   RFAM; RF00276.


  [Part of this file has been deleted for brevity]

     ttggccccac cccagcatgt ctccaggttc ctctcagccc tggttccttt tggccctgca   222690
0
     gtcacaatgg gcaacactgt gacgcaccct gtcctgtgtc acagtgtcat acactcaggc   222696
0
     tcacattgcc cctaggccac ttgccagcca agggacatgg ccacattttg tgtcttctgc   222702
0
     acctcagcct tgctttcaag tgcaggtgat gatggcaccc acgcagaaca aatgttattt   222708
0
     gctatcttcg tcgagtttag tcatccaatt ttccaaccct cactgggcaa ggaagagtgt   222714
0
     ggtttccacc aagaaggcag gatgtcagca gtcacagggg caaccaacag ggaaagccgc   222720
0
     cggaaaatag accccacagg aagcacaggt gtccagtgga gatgggaacc ctgcagattt   222726
0
     gaccgtcttt aagcagatta gagagattac cgttactaac aacttagcca taaaagttta   222732
0
     ttagctattt tcaaaaagca taaaattatg taatataatt ttttttaaat ttccatcaat   222738
0
     acaaaactaa tctgggcact gcaacttccg gtgggcaact gggataggcg gcatcatcag   222744
0
     gaaggcgagc cctgccgtgc cccatgtgcc agtgccccag atggcggcag cctccccaga   222750
0
     agcaccttgt atctcccctg cacagggcca gggtcccagc ttcccataca ccttctcctg   222756
0
     ctttttcttt tctgtccttt cctttttcaa taaaccacct gcaaaaaggg aaaaccattc   222762
0
     tgaggacaag aaacatgtca atgggaaata cacagttgcc agagggtaaa aggccctgtt   222768
0
     cattctcatt gaaaagctca ggtatttctg ttaaagtctc tccttttact ttaggatgct   222774
0
     gactcctgcg tccatctcaa cctgggcatc gtgccaccac cttcaagaag agaaaaacta   222780
0
     agtagtgctt tgcaaagggg cagcagcatt tctcatttct gaccatgtca ggcacatggc   222786
0
     catgcagatg agcaggtggg ggacacaggt gagtctccag acctgctctc ctcccacagt   222792
0
     acattcttga gtctttttaa acagttgtga aaatgccaca gatgcaagca cctgtgggcc   222798
0
     actcccatgg ggaccgttgc acaaggcagt gccactcatt ctcagaacct cctaccatgg   222804
0
     gctatgctta gtgacccgag gccaagccaa ggaagacgcc agccacaggg tgccatcctc   222810
0
     aggggcatgc tgccagcagg ggcaaagtta tccctagcaa caagatacag aaagaaagaa   222816
0
     aaaaggaagg aaatgtagcc aatgggccgg ttcaggttct tgactttgcc acacaaaaga   222822
0
     atttgagagc aagtccaaag taaaagtcag caagagaatt tattgcaaag tgaaagtaca   222828
0
     ctctgacagc tgatcagagc agctgctcaa aagagagaca gtaccctccc ctcacgggag   222834
0
     tcttacatga ttattcatga ataggtggga aggggtattg ttttaagcat gttctgtggt   222840
0
     ctcttgaacg tgcatgcact gtggttgtac atatcagcac acacatctta cgtctcatta   222846
0
     gcatcttaac ttccctctca gagttgtgtt tgctactatt gtaatgagca taggtcagcc   222852
0
     caaggacact attcatgggt ttctgggctt cctcagatgt ggggatgcct cccttggctc   222858
0
     ttctacctct ttgctgcagg atgttctaac cacaagccca ggatatggtt tgcgcactgt   222864
0
     cgaacagctt gttctctcca tcaacctgac aagtctcttg tttcctttca agggaggctg   222870
0
     tgaacaccct atctcactga cctcagaagg acagtacagc agtagccacc atgaccaaaa   222876
0
     agatgattcc agaagtgcag gacaactccc tacccagagg ctgtggctgt gcagtaacac   222882
0
     accaagaggg gagtccagct ggctctcagg gtgctcacta ccctcatctg ggggcctgga   222888
0
     ggacgtcaat tcctgagaac gccacgttct agtgagtaga atgaactgag agatacacag   222894
0
     caaagctcca catacttttc cttttctttg tgcccgcagt gttcttcatc agtgtgctct   222900
0
     cgcttttcag ctactactgt tggctggctg gaaaaaatag aacaatagta aaaattagag   222906
0
     accagtcttt ggtgatgaag agaaatattg gctacttcca gtattttcta gctttggtta   222912
0
     tggttgcagt tttccagctc accttgtggg gatgaattca gaaaaaagtt acaaattgaa   222918
0
     atgaacatgc cagaagtatt ggctcaaatc aacgttgtcc tattaagcca cttagtgaat   222924
0
     caaaagaccg cttgttggac tgttaatctc ggtggccaga gaaaggagct gaagaaggtg   222930
0
     ttgccagatc aggaacaaat aattacagcg gcaatagaaa atggaagacc acttgttcat   222936
0
     aaccatttga ataagggcaa ggtgtatgga aacacattat gaactgatat tttcagtttt   222942
0
     gtttgcaaga aaatgattaa taaggtgaaa taattgaagt atcacggaag atacattaaa   222948
0
     aaaaaaaaaa gcctttgtac agtttgctgg agccacagat gtcctactcc agagcagaac   222954
0
     aatgcctgaa tcttcagggt ccatttctgc cgcattcact agcaaccaca aatgtgactt   222960
0
     aattttactt tggaaataat gcttacccat tgtgagatgc tgtaatatga accatcatta   222966
0
     catgttaaca tggcacatgg aattttgagt gtctaagtta catttttaga gttgtttctt   222972
0
     agtagccatg tgagtttcca ctccaaaaac acaagctaaa aacttgtttt gagtgaagga   222978
0
     catctagggc aaatggtggc tgaaagtgaa tgagatc                            222981
7
//

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 (gwilliam © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

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
