|
|
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: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
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 |
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
//
|
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
//
|
With the -data qualifier a file of the positions of the matches in the minimal non-overlapping set of matches is output.
| 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.