| dotpath

## Function

Displays a non-overlapping wordmatch dotplot of two 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 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.

dotpath is very similar to the program dottup which looks for places where words (tuples) of a specified length have an exact match in both sequences and draws a diagonal line over the position of these words.

Using a longer word size thus displays less random noise, runs extremely quickly, but is less sensitive.

dotpath finds all matches of size -wordsize or greater between two sequences. It then reduces the matches found to the minimal set of long matches that do not overlap. This is a way of finding the (nearly) optimal path aligning two sequences. It is not the true optimal path as produced by the algorithms used in water or needle, but for very closely related sequences it will produce the same result and will work well with very long sequences.

If you wish to compare the path found by dotpath to the set of all matches found then the qualifier -overlaps will show all matches in red except for the matches in the minimal path which are shown in black, as normal.

## Usage

Here is a sample session with dotpath

    % dotpath tembl:AF129756 tembl:AP000504 -word 20 -graph cps -overlaps
    Displays 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

       Mandatory qualifiers (* if not always prompted):
      [-sequencea]         sequence   Sequence USA
      [-sequenceb]         sequence   Sequence USA
       -wordsize           integer    Word size
    *  -graph              graph      Graph type
    *  -outfile            outfile    Output file name

       Optional qualifiers:
       -overlaps           boolean    Displays the overlapping matches (in red) as
                                      well as the minimal set of non-overlapping
                                      matches
       -[no]boxit          boolean    Draw a box around dotplot

       Advanced qualifiers:
       -data               boolean    Output the match data to a file instead of
                                      plotting it

       Associated qualifiers:
      "-sequencea" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -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
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-sequenceb" related qualifiers
       -sbegin2             integer    First base used
       -send2               integer    Last base used, def=seq length
       -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
       -sopenfile2          string     Input filename
       -sdbname2            string     Database name
       -sid2                string     Entryname
       -ufo2                string     UFO features
       -fformat2            string     Features format
       -fopenfile2          string     Features file name
      "-graph" related qualifiers
       -gprompt             boolean    Graph prompting
       -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
      "-outfile" related qualifiers
       -odirectory          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 required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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 deaths

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequencea] (Parameter 1) | Sequence USA | Readable sequence | Required
[-sequenceb] (Parameter 2) | Sequence USA | Readable sequence | Required
-wordsize | Word size | Integer 2 or more | 4
-graph | Graph type | EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm, png | EMBOSS_GRAPHICS value, or x11
-outfile | Output file name | Output file | <sequence>.dotpath
Optional qualifiers | Allowed values | Default
-overlaps | Displays the overlapping matches (in red) as well as the minimal set of non-overlapping matches | Boolean value Yes/No | No
-[no]boxit | Draw a box around dotplot | Boolean value Yes/No | Yes
Advanced qualifiers | Allowed values | Default
-data | Output the match data to a file instead of plotting it | Boolean value Yes/No | No

## 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   standard; DNA; HUM; 184666 BP.
    XX
    AC   AF129756;
    XX
    SV   AF129756.1
    XX
    DT   12-MAR-1999 (Rel. 59, Created)
    DT   29-OCT-1999 (Rel. 61, Last updated, Version 2)
    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; Primates; Catarrhini; Hominidae; Homo.
    XX
    RN   [1]
    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   [2]
    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   [3]
    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
    XX
    DR   EPD; EP11158; HS_TNFA.
    DR   EPD; EP11159; HS_TNFB.
    DR   SPTREMBL; O00452; O00452.
    DR   SPTREMBL; O14931; O14931.
    DR   SPTREMBL; O95866; O95866.
    DR   SPTREMBL; O95868; O95868.
    DR   SPTREMBL; O95869; O95869.
    DR   SPTREMBL; O95870; O95870.

      [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:AP000504

    ID   AP000504   standard; DNA; HUM; 100000 BP.
    XX
    AC   AP000504; BA000025;
    XX
    SV   AP000504.1
    XX
    DT   28-SEP-1999 (Rel. 61, Created)
    DT   22-AUG-2001 (Rel. 68, Last updated, Version 3)
    XX
    DE   Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section
    DE   3/20.
    XX
    KW   .
    XX
    OS   Homo sapiens (human)
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
    OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
    XX
    RN   [1]
    RP   1-100000
    RA   Hirakawa M., Yamaguchi H., Imai K., Shimada J.;
    RT   ;
    RL   Submitted (21-SEP-1999) 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   SWISS-PROT; O00299; CLI1_HUMAN.
    DR   SWISS-PROT; O43196; MSH5_HUMAN.
    DR   SWISS-PROT; O95445; APOM_HUMAN.
    DR   SWISS-PROT; O95865; DDH2_HUMAN.
    DR   SWISS-PROT; O95867; NG24_HUMAN.
    DR   SWISS-PROT; P13862; KC2B_HUMAN.
    XX
    CC   This sequence is conducted by Tokai University as a JST sequencing
    CC   Team.
    CC   Principal Investigator: Hidetoshi Inoko Ph.D
    CC   Phone:+81-463-93-1121, Fax:+81-463-94-8884,
    CC   The sequence is submitted by Human Genome Sequencing in ALIS
    CC   project of JST
    CC   Japan Science and Technology Corporation (JST)
    CC   5-3, Yonbancyo, Chiyoda-ku, Tokyo, 102-0081 Japan
    CC   For further infomation about this sequences, please visit our
    CC   sequence archive Web site (http://www-alis.tokyo.jst.go.jp/HGS/top.

      [Part of this file has been deleted for brevity]

         gggtggatca tgaggtcaag agatcgagac tatcctggct aacatgatga aaccccgtct     97080
         ctactaaaaa tacaaaaaat tagctgggca tggtggcggg cacctgtagt cccagctact     97140
         cgggaggctg agtcaggaga atggtgtgaa cccaggagac ggagcttgca gtgagctgag     97200
         gtcgcaccac tgcactccag cctgggtgat agagcgagac tctgtctcaa aaaaaaaaaa     97260
         aaaaaaaaaa aaaacaaaaa ttagccgggt gtggtggcag gcaacttaat cccagctact     97320
         tgggaggcag aggcaggaga atcgtttgaa cctgggaggc ggaggttgaa gagaatagaa     97380
         gctctgctgg tccagagaag gattgggcca gggctctggg agaccaggga gaaagagggc     97440
         acatgtggtc cctgttgact gtgagggtgg gaatctgagg aaggctttgg ctcattgccc     97500
         cttgggtttg tccacagcca tccttcccct gcggagtatg tcgaggtgct ccaggagcta     97560
         cagcggctgg agagtcgcct ccagcccttc ttgcagcgct actacgaggt tctgggtgct     97620
         gctgccacca cggactacaa taacaatgtg agccctttga tggccctgcc ctttctcctc     97680
         agccccagta ctcccaaaac agaacaggct gaaatacaga taactctttc cctccctgga     97740
         aaaacattgc aacagggcca ggtgcagtgg ctcacgcctg taatcccagc actttgggag     97800
         gccaaggtgg gcggatcatc tgagatcggg agtttgagac cagcctggcc aacatggtgc     97860
         aaccccatct ctactgaaaa tataaacatt agctggatgt agtggtgcac acctgtaatc     97920
         ccagctactc aggaggctga ggcaggagaa tcgctagaac tcgggaggag ggggttgcag     97980
         tgagccgaga ttgcactact gcactctagc ctgggtgaca gagcgagact gtctcaaaaa     98040
         acaaaacaaa acaaaaaaac acacattgca acaaaacaat ttctctctaa acctgtaagt     98100
         gattttgtcc tcccttacag agaaggtgat aatctttgct gtaagcactg tcctcgtatc     98160
         gtaccccttg tgcccctgaa tgaatttaga aaatgtaaag tacaggagat cagtatatga     98220
         tgacttactg attcatagta gtgttttaat aggatgttcc ttatgtgaat aagatataat     98280
         ttatttgcaa agatttggtc tacatgtaaa cttccaagga tataactgaa agttttggag     98340
         gacatggtat tctcagtagg cattattgct tttattagtg agatggactc cagcttgata     98400
         ttttctgcct ttttgtgttt ggctggttgt gcgcagcacg agggccggga ggaggatcag     98460
         cggttgatca acttggtagg ggagagcctg cgactgctgg gcaacacctt tgttgcactg     98520
         tctgacctgc gctgcaatct ggcctgcacg cccccacgac acctgcatgt ggtccggcct     98580
         atgtctcact acaccacccc catggtgctc cagcaggcag ccattcccat acaggtgggt     98640
         tagggggagt ctggcctgag ggagagtgag gggtgttgat agagtgaccc agggtagcta     98700
         ctgggcctga aggaggttag gaaaggagga gactggaaac atggtgatga aggctggaga     98760
         tactttagag gtttatcatg aggttttctt ggttaggctc ttgtattttt ctcacatctg     98820
         cctgtccatc tgtctttttc agatcaatgt gggaaccact gtgaccatga caggaaatgg     98880
         gactcggccc cccccaactc ccaatgcaga ggcacctccc cctggtcctg ggcaggcctc     98940
         atccgtggct ccgtcttcta ccaatgtcga gtcctcagct gagggggctc ccccgccagg     99000
         tccagctccc ccgccagcca ccagccaccc gagggtcatc cggatttccc accagagtgt     99060
         ggaacccgtg gtcatgatgc acatgaacat tcaaggtgag aatagttgct ggcgagaaga     99120
         gcaggatcag catgatgagg gaggttcatg ctgaggtgtg agggaacagg gtggggaagg     99180
         gagaggcaca tgctggtggt ggtagcctgg ggaccagagc agaagcttaa gtagacagat     99240
         gtggggggtg tgggggttgg tttgtctttg gaggtgtgtt tgtgtggtga agggagtacc     99300
         tctccctgtt tagatggagg gaaaggcagg ctttctgatt gggggattat gggcctgaag     99360
         tatgcctgat ctcagaagga tatagttagg ccttggccct acctacctca gggccactgt     99420
         ctctgtctcc ctgcccagat tctggcacac agcctggtgg tgttccgagt gctcccactg     99480
         gccccctggg accccctggt catggccaaa ccctgggtaa gagtgagggc atcagggcag     99540
         gctgagctct gggtagagaa agggaagggc tgagtgggtg ggttgaaggg gtccaggttc     99600
         aaggttacat cagacccgcc ccccaggctc caccctcatc cagctgccct ccctgccccc     99660
         tgagttcatg cacgccgtcg cccaccagat cactcatcag gccatggtgg cagctgttgc     99720
         ctccgcggcc gcaggtaatg acctggaagg ggaggcttgg gaggtagggc acagtccatg     99780
         gtggcagctg gctggcaagg gcctggccct cagccctctt cggtctgtct cttctgccac     99840
         ccacaggaca gcaggtgcca ggcttcccaa cagctccaac ccgggtggtg attgcccggc     99900
         ccactcctcc acaggctcgg ccttcccatc ctggagggcc cccagtctct gggacactgg     99960
         tgagcaaggg tcggggagtt ctagtgcgta acagtctagg                          100000
    //

## 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

## Data files

## Notes

## References

## 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

## Exit status

## Known bugs

## See also

Program name | Description
--- | ---
dotmatcher | Displays a thresholded dotplot of two sequences
dottup | Displays a wordmatch dotplot of two sequences
polydot | Displays all-against-all dotplots of a set of sequences

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 © hgmp.mrc.ac.uk)
HGMP-RC, 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