| dottup

## Function

Displays a 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 (in the simplest forms of dotplot) 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 as these will have long diagonal lines. 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).

dottup 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. This is a fast, but not especially sensitive way of creating dotplots. It is an acceptable method for displaying regions of substantial similarity between two sequences.

Using a longer word (tuple) size displays less random noise, runs extremely quickly, but is less sensitive. Shorter word sizes are more sensitive to shorter or fragmentary regions of similarity, but also display more random points of similarity (noise) and runs slower.

## Usage

Here is a sample session with dottup

    % dottup tembl:j01636 tembl:v00294 -wordsize=6 -gtitle="v00294 vs j01636" -graph cps
    Displays a wordmatch dotplot of two sequences

    Created dottup.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):
      [-asequence]         sequence   Sequence filename and optional format, or
                                      reference (input USA)
      [-bsequence]         sequence   Sequence filename and optional format, or
                                      reference (input USA)
       -wordsize           integer    [10] Word size (Integer 2 or more)
    *  -graph              graph      [$EMBOSS_GRAPHICS value, or x11] Graph type
                                      (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                      tekt, tek, none, data, xterm, png, gif)
    *  -xygraph            xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                      (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                      tekt, tek, none, data, xterm, png, gif)

       Additional (Optional) qualifiers (* if not always prompted):
    *  -[no]boxit          boolean    [Y] Draw a box around dotplot

       Advanced (Unprompted) qualifiers:
       -stretch            toggle     [N] Use non-proportional axes

       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

       "-xygraph" 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

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-asequence] (Parameter 1) | Sequence filename and optional format, or reference (input USA) | Readable sequence | Required
[-bsequence] (Parameter 2) | Sequence filename and optional format, or reference (input USA) | Readable sequence | Required
-wordsize | Word size | Integer 2 or more | 10
-graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11
-xygraph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers | Allowed values | Default
-[no]boxit | Draw a box around dotplot | Boolean value Yes/No | Yes
Advanced (Unprompted) qualifiers | Allowed values | Default
-stretch | Use non-proportional axes | Toggle value Yes/No | No

## Input file format

Any two sequence USAs of the same type (DNA or protein).

### Input files for usage example

'tembl:j01636' is a sequence entry in the example nucleic acid database 'tembl'

### Database entry: tembl:j01636

    ID   J01636; SV 1; linear; genomic DNA; STD; PRO; 7477 BP.
    XX
    AC   J01636; J01637; K01483; K01793;
    XX
    DT   30-NOV-1990 (Rel. 26, Created)
    DT   09-SEP-2004 (Rel. 81, Last updated, Version 8)
    XX
    DE   E.coli lactose operon with lacI, lacZ, lacY and lacA genes.
    XX
    KW   acetyltransferase; beta-D-galactosidase; galactosidase; lac operon;
    KW   lac repressor protein; lacA gene; lacI gene; lactose permease; lacY gene;
    KW   lacZ gene; mutagenesis; palindrome; promoter region;
    KW   thiogalactoside acetyltransferase.
    XX
    OS   Escherichia coli
    OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
    OC   Enterobacteriaceae; Escherichia.
    XX
    RN   [1]
    RP   1243-1266
    RX   PUBMED; 4587255.
    RA   Gilbert W., Maxam A.;
    RT   "The nucleotide sequence of the lac operator";
    RL   Proc. Natl. Acad. Sci. U.S.A. 70(12):3581-3584(1973).
    XX
    RN   [2]
    RP   1246-1308
    RX   PUBMED; 4587256.
    RA   Maizels N.M.;
    RT   "The nucleotide sequence of the lactose messenger ribonucleic acid
    RT   transcribed from the UV5 promoter mutant of Escherichia coli";
    RL   Proc. Natl. Acad. Sci. U.S.A. 70(12):3585-3589(1973).
    XX
    RN   [3]
    RX   PUBMED; 4598642.
    RA   Gilbert W., Maizels N., Maxam A.;
    RT   "Sequences of controlling regions of the lactose operon";
    RL   Cold Spring Harb. Symp. Quant. Biol. 38:845-855(1974).
    XX
    RN   [4]
    RA   Gilbert W., Gralla J., Majors A.J., Maxam A.;
    RT   "Lactose operator sequences and the action of lac repressor";
    RL   (in) Sund H., Blauer G. (Eds.);
    RL   PROTEIN-LIGAND INTERACTIONS:193-207;
    RL   Walter de Gruyter, New York (1975)
    XX
    RN   [5]
    RP   1146-1282
    RX   PUBMED; 1088926.
    RA   Dickson R.C., Abelson J.N., Barnes W.M., Reznikoff W.S.;

      [Part of this file has been deleted for brevity]

         cgatttggct acatgacatc aaccatatca gcaaaagtga tacgggtatt atttttgccg      4560
         ctatttctct gttctcgcta ttattccaac cgctgtttgg tctgctttct gacaaactcg      4620
         ggctgcgcaa atacctgctg tggattatta ccggcatgtt agtgatgttt gcgccgttct      4680
         ttatttttat cttcgggcca ctgttacaat acaacatttt agtaggatcg attgttggtg      4740
         gtatttatct aggcttttgt tttaacgccg gtgcgccagc agtagaggca tttattgaga      4800
         aagtcagccg tcgcagtaat ttcgaatttg gtcgcgcgcg gatgtttggc tgtgttggct      4860
         gggcgctgtg tgcctcgatt gtcggcatca tgttcaccat caataatcag tttgttttct      4920
         ggctgggctc tggctgtgca ctcatcctcg ccgttttact ctttttcgcc aaaacggatg      4980
         cgccctcttc tgccacggtt gccaatgcgg taggtgccaa ccattcggca tttagcctta      5040
         agctggcact ggaactgttc agacagccaa aactgtggtt tttgtcactg tatgttattg      5100
         gcgtttcctg cacctacgat gtttttgacc aacagtttgc taatttcttt acttcgttct      5160
         ttgctaccgg tgaacagggt acgcgggtat ttggctacgt aacgacaatg ggcgaattac      5220
         ttaacgcctc gattatgttc tttgcgccac tgatcattaa tcgcatcggt gggaaaaacg      5280
         ccctgctgct ggctggcact attatgtctg tacgtattat tggctcatcg ttcgccacct      5340
         cagcgctgga agtggttatt ctgaaaacgc tgcatatgtt tgaagtaccg ttcctgctgg      5400
         tgggctgctt taaatatatt accagccagt ttgaagtgcg tttttcagcg acgatttatc      5460
         tggtctgttt ctgcttcttt aagcaactgg cgatgatttt tatgtctgta ctggcgggca      5520
         atatgtatga aagcatcggt ttccagggcg cttatctggt gctgggtctg gtggcgctgg      5580
         gcttcacctt aatttccgtg ttcacgctta gcggccccgg cccgctttcc ctgctgcgtc      5640
         gtcaggtgaa tgaagtcgct taagcaatca atgtcggatg cggcgcgacg cttatccgac      5700
         caacatatca taacggagtg atcgcattga acatgccaat gaccgaaaga ataagagcag      5760
         gcaagctatt taccgatatg tgcgaaggct taccggaaaa aagacttcgt gggaaaacgt      5820
         taatgtatga gtttaatcac tcgcatccat cagaagttga aaaaagagaa agcctgatta      5880
         aagaaatgtt tgccacggta ggggaaaacg cctgggtaga accgcctgtc tatttctctt      5940
         acggttccaa catccatata ggccgcaatt tttatgcaaa tttcaattta accattgtcg      6000
         atgactacac ggtaacaatc ggtgataacg tactgattgc acccaacgtt actctttccg      6060
         ttacgggaca ccctgtacac catgaattga gaaaaaacgg cgagatgtac tcttttccga      6120
         taacgattgg caataacgtc tggatcggaa gtcatgtggt tattaatcca ggcgtcacca      6180
         tcggggataa ttctgttatt ggcgcgggta gtatcgtcac aaaagacatt ccaccaaacg      6240
         tcgtggcggc tggcgttcct tgtcgggtta ttcgcgaaat aaacgaccgg gataagcact      6300
         attatttcaa agattataaa gttgaatcgt cagtttaaat tataaaaatt gcctgatacg      6360
         ctgcgcttat caggcctaca agttcagcga tctacattag ccgcatccgg catgaacaaa      6420
         gcgcaggaac aagcgtcgca tcatgcctct ttgacccaca gctgcggaaa acgtactggt      6480
         gcaaaacgca gggttatgat catcagccca acgacgcaca gcgcatgaaa tgcccagtcc      6540
         atcaggtaat tgccgctgat actacgcagc acgccagaaa accacggggc aagcccggcg      6600
         atgataaaac cgattccctg cataaacgcc accagcttgc cagcaatagc cggttgcaca      6660
         gagtgatcga gcgccagcag caaacagagc ggaaacgcgc cgcccagacc taacccacac      6720
         accatcgccc acaataccgg caattgcatc ggcagccaga taaagccgca gaaccccacc      6780
         agttgtaaca ccagcgccag cattaacagt ttgcgccgat cctgatggcg agccatagca      6840
         ggcatcagca aagctcctgc ggcttgccca agcgtcatca atgccagtaa ggaaccgctg      6900
         tactgcgcgc tggcaccaat ctcaatatag aaagcgggta accaggcaat caggctggcg      6960
         taaccgccgt taatcagacc gaagtaaaca cccagcgtcc acgcgcgggg agtgaatacc      7020
         acgcgaaccg gagtggttgt tgtcttgtgg gaagaggcga cctcgcgggc gctttgccac      7080
         caccaggcaa agagcgcaac aacggcaggc agcgccacca ggcgagtgtt tgataccagg      7140
         tttcgctatg ttgaactaac cagggcgtta tggcggcacc aagcccaccg ccgcccatca      7200
         gagccgcgga ccacagcccc atcaccagtg gcgtgcgctg ctgaaaccgc cgtttaatca      7260
         ccgaagcatc accgcctgaa tgatgccgat ccccacccca ccaagcagtg cgctgctaag      7320
         cagcagcgca ctttgcgggt aaagctcacg catcaatgca ccgacggcaa tcagcaacag      7380
         actgatggcg acactgcgac gttcgctgac atgctgatga agccagcttc cggccagcgc      7440
         cagcccgccc atggtaacca ccggcagagc ggtcgac                               7477
    //

### Database entry: tembl:v00294

    ID   V00294; SV 1; linear; genomic DNA; STD; PRO; 1113 BP.
    XX
    AC   V00294;
    XX
    DT   09-JUN-1982 (Rel. 01, Created)
    DT   10-FEB-1999 (Rel. 58, Last updated, Version 2)
    XX
    DE   E. coli laci gene (codes for the lac repressor).
    XX
    KW   DNA binding protein; repressor.
    XX
    OS   Escherichia coli
    OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
    OC   Enterobacteriaceae; Escherichia.
    XX
    RN   [1]
    RP   1-1113
    RX   DOI; 10.1038/274765a0.
    RX   PUBMED; 355891.
    RA   Farabaugh P.J.;
    RT   "Sequence of the lacI gene";
    RL   Nature 274(5673):765-769(1978).
    XX
    CC   KST ECO.LACI
    XX
    FH   Key             Location/Qualifiers
    FH
    FT   source          1..1113
    FT                   /organism="Escherichia coli"
    FT                   /mol_type="genomic DNA"
    FT                   /db_xref="taxon:562"
    FT   CDS             31..1113
    FT                   /transl_table=11
    FT                   /note="reading frame"
    FT                   /db_xref="GOA:P03023"
    FT                   /db_xref="PDB:1CJG"
    FT                   /db_xref="PDB:1EFA"
    FT                   /db_xref="PDB:1JWL"
    FT                   /db_xref="PDB:1JYE"
    FT                   /db_xref="PDB:1JYF"
    FT                   /db_xref="PDB:1L1M"
    FT                   /db_xref="PDB:1LBG"
    FT                   /db_xref="PDB:1LBH"
    FT                   /db_xref="PDB:1LBI"
    FT                   /db_xref="PDB:1LCC"
    FT                   /db_xref="PDB:1LCD"
    FT                   /db_xref="PDB:1LQC"
    FT                   /db_xref="PDB:1LTP"
    FT                   /db_xref="PDB:1TLF"
    FT                   /db_xref="PDB:2BJC"
    FT                   /db_xref="UniProtKB/Swiss-Prot:P03023"
    FT                   /protein_id="CAA23569.1"
    FT                   /translation="MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAEL
    FT                   NYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGV
    FT                   EACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSH
    FT                   EDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSA
    FT                   MSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSC
    FT                   YIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPR
    FT                   ALADSLMQLARQVSRLESGQ"
    XX
    SQ   Sequence 1113 BP; 249 A; 304 C; 322 G; 238 T; 0 other;
         ccggaagaga gtcaattcag ggtggtgaat gtgaaaccag taacgttata cgatgtcgca        60
         gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg tgaaccaggc cagccacgtt       120
         tctgcgaaaa cgcgggaaaa agtggaagcg gcgatggcgg agctgaatta cattcccaac       180
         cgcgtggcac aacaactggc gggcaaacag tcgttgctga ttggcgttgc cacctccagt       240
         ctggccctgc acgcgccgtc gcaaattgtc gcggcgatta aatctcgcgc cgatcaactg       300
         ggtgccagcg tggtggtgtc gatggtagaa cgaagcggcg tcgaagcctg taaagcggcg       360
         gtgcacaatc ttctcgcgca acgcgtcagt gggctgatca ttaactatcc gctggatgac       420
         caggatgcca ttgctgtgga agctgcctgc actaatgttc cggcgttatt tcttgatgtc       480
         tctgaccaga cacccatcaa cagtattatt ttctcccatg aagacggtac gcgactgggc       540
         gtggagcatc tggtcgcatt gggtcaccag caaatcgcgc tgttagcggg cccattaagt       600
         tctgtctcgg cgcgtctgcg tctggctggc tggcataaat atctcactcg caatcaaatt       660
         cagccgatag cggaacggga aggcgactgg agtgccatgt ccggttttca acaaaccatg       720
         caaatgctga atgagggcat cgttcccact gcgatgctgg ttgccaacga tcagatggcg       780
         ctgggcgcaa tgcgcgccat taccgagtcc gggctgcgcg ttggtgcgga tatctcggta       840
         gtgggatacg acgataccga agacagctca tgttatatcc cgccgtcaac caccatcaaa       900
         caggattttc gcctgctggg gcaaaccagc gtggaccgct tgctgcaact ctctcagggc       960
         caggcggtga agggcaatca gctgttgccc gtctcactgg tgaaaagaaa aaccaccctg      1020
         gcgcccaata cgcaaaccgc ctctccccgc gcgttggccg attcattaat gcagctggca      1080
         cgacaggttt cccgactgga aagcgggcag tga                                   1113
    //

## Output file format

An image is output to the requested output device.

### Output files for usage example

### Graphics File: dottup.ps

## Data files

None.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

0 upon successful completion.

## Known bugs

None.

## See also

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

dotmatcher, by comparison, moves a window of specified length up each diagonal and displays a line over the window if the sum of the comparisons (using a substitution matrix) exceeds a threshold. It is slower but much more sensitive.

## Author(s)

Ian Longden (il © sanger.ac.uk)
Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## History

Completed 24th March 1999.

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None