Appdoc:Dotpath

From EMBOSS

Contents 1 Function 2 Description 3 Algorithm 4 Usage 5 Command line arguments 6 Input file format 6.1 Input example 6.1.1 Database entry: tembl:AF129756 6.1.2 Database entry: tembl:BA000025 7 Output file format 7.1 Output example 7.1.1 Graphics File: dotpath.ps 8 Notes 9 References 10 Warnings 11 Diagnostic Error Messages 12 Exit status 13 Known bugs 14 See also 15 Author(s) 16 History 17 Target users 18 Comments

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

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-asequence] (Parameter 1)	sequence	Sequence filename and optional format, or reference (input USA)	Readable sequence	Required
[-bsequence] (Parameter 2)	sequence	Sequence filename and optional format, or reference (input USA)	Readable sequence	Required
-wordsize	integer	Word size	Integer 2 or more	4
-graph	graph	Graph type	EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, das, xterm, png, gif	EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers
-overlaps	boolean	Displays the overlapping matches (in red) as well as the minimal set of non-overlapping matches	Boolean value Yes/No	No
-[no]boxit	boolean	Draw a box around dotplot	Boolean value Yes/No	Yes
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-asequence" associated sequence qualifiers
-sbegin1 -sbegin_asequence	integer	Start of the sequence to be used	Any integer value	0
-send1 -send_asequence	integer	End of the sequence to be used	Any integer value	0
-sreverse1 -sreverse_asequence	boolean	Reverse (if DNA)	Boolean value Yes/No	N
-sask1 -sask_asequence	boolean	Ask for begin/end/reverse	Boolean value Yes/No	N
-snucleotide1 -snucleotide_asequence	boolean	Sequence is nucleotide	Boolean value Yes/No	N
-sprotein1 -sprotein_asequence	boolean	Sequence is protein	Boolean value Yes/No	N
-slower1 -slower_asequence	boolean	Make lower case	Boolean value Yes/No	N
-supper1 -supper_asequence	boolean	Make upper case	Boolean value Yes/No	N
-sformat1 -sformat_asequence	string	Input sequence format	Any string
-sdbname1 -sdbname_asequence	string	Database name	Any string
-sid1 -sid_asequence	string	Entryname	Any string
-ufo1 -ufo_asequence	string	UFO features	Any string
-fformat1 -fformat_asequence	string	Features format	Any string
-fopenfile1 -fopenfile_asequence	string	Features file name	Any string
"-bsequence" associated sequence qualifiers
-sbegin2 -sbegin_bsequence	integer	Start of the sequence to be used	Any integer value	0
-send2 -send_bsequence	integer	End of the sequence to be used	Any integer value	0
-sreverse2 -sreverse_bsequence	boolean	Reverse (if DNA)	Boolean value Yes/No	N
-sask2 -sask_bsequence	boolean	Ask for begin/end/reverse	Boolean value Yes/No	N
-snucleotide2 -snucleotide_bsequence	boolean	Sequence is nucleotide	Boolean value Yes/No	N
-sprotein2 -sprotein_bsequence	boolean	Sequence is protein	Boolean value Yes/No	N
-slower2 -slower_bsequence	boolean	Make lower case	Boolean value Yes/No	N
-supper2 -supper_bsequence	boolean	Make upper case	Boolean value Yes/No	N
-sformat2 -sformat_bsequence	string	Input sequence format	Any string
-sdbname2 -sdbname_bsequence	string	Database name	Any string
-sid2 -sid_bsequence	string	Entryname	Any string
-ufo2 -ufo_bsequence	string	UFO features	Any string
-fformat2 -fformat_bsequence	string	Features format	Any string
-fopenfile2 -fopenfile_bsequence	string	Features file name	Any string
"-graph" associated graph qualifiers
-gprompt	boolean	Graph prompting	Boolean value Yes/No	N
-gdesc	string	Graph description	Any string
-gtitle	string	Graph title	Any string	Dotpath: $(asequence.usa) vs $(bsequence.usa)
-gsubtitle	string	Graph subtitle	Any string
-gxtitle	string	Graph x axis title	Any string	$(bsequence.name)
-gytitle	string	Graph y axis title	Any string	$(asequence.name)
-goutfile	string	Output file for non interactive displays	Any string
-gdirectory	string	Output directory	Any string
General qualifiers
-auto	boolean	Turn off prompts	Boolean value Yes/No	N
-stdout	boolean	Write first file to standard output	Boolean value Yes/No	N
-filter	boolean	Read first file from standard input, write first file to standard output	Boolean value Yes/No	N
-options	boolean	Prompt for standard and additional values	Boolean value Yes/No	N
-debug	boolean	Write debug output to program.dbg	Boolean value Yes/No	N
-verbose	boolean	Report some/full command line options	Boolean value Yes/No	Y
-help	boolean	Report command line options. More information on associated and general qualifiers can be found with -help -verbose	Boolean value Yes/No	N
-warning	boolean	Report warnings	Boolean value Yes/No	Y
-error	boolean	Report errors	Boolean value Yes/No	Y
-fatal	boolean	Report fatal errors	Boolean value Yes/No	Y
-die	boolean	Report dying program messages	Boolean value Yes/No	Y

Input file format

Input 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; HLA02802; V*01010102.
DR   RFAM; RF00994; mir-1255.
DR   UniProtKB/Swiss-Prot; P59942; MCCD1_HUMAN.
XX
CC   This sequence is conducted by Tokai University as a JST sequencing
CC   Team.


  [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 example

Graphics File: dotpath.ps

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

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 (@) 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