|
|
dotpath |
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.
% dotpath tembl:AF129756 tembl:BA000025 -word 20 -graph cps -overlaps 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
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 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 | 4 |
| -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 |
| Additional (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 (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
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
//
|
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 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
//
|
With the -data qualifier a file of the positions of the matches in the minimal non-overlapping set of matches is output.
![[dotpath results]](dotpath.1.dotpath.gif)
| 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.