dottup |
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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.
% 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
Displays a wordmatch dotplot of two sequences Version: EMBOSS:6.4.0.0 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 [$EMBOSS_GRAPHICS value, or x11] Graph type (ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg) * -xygraph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type (ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg) 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 first file to standard output -filter boolean Read first file from standard input, write first file to 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 and exit. 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 -version boolean Report version number and exit |
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 | 10 |
-graph | graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg | EMBOSS_GRAPHICS value, or x11 |
-xygraph | xygraph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg | EMBOSS_GRAPHICS value, or x11 |
Additional (Optional) qualifiers | ||||
-[no]boxit | boolean | Draw a box around dotplot | Boolean value Yes/No | Yes |
Advanced (Unprompted) qualifiers | ||||
-stretch | toggle | Use non-proportional axes | Toggle value Yes/No | No |
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 | Dottup: $(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 | |
"-xygraph" associated xygraph qualifiers | ||||
-gprompt | boolean | Graph prompting | Boolean value Yes/No | N |
-gdesc | string | Graph description | Any string | |
-gtitle | string | Graph title | Any string | Dottup (stretched): $(asequence.usa) vs $(bsequence.usa) |
-gsubtitle | string | Graph subtitle | Any string | |
-gxtitle | string | Graph x axis title | Any string | |
-gytitle | string | Graph y axis title | Any string | |
-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 and exit. 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 |
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
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 DOI; 10.1073/pnas.70.12.3581. 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 DOI; 10.1073/pnas.70.12.3585. 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 [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 // |
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="InterPro:IPR000843" FT /db_xref="InterPro:IPR001761" FT /db_xref="InterPro:IPR010982" 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:1OSL" FT /db_xref="PDB:1TLF" FT /db_xref="PDB:1Z04" FT /db_xref="PDB:2BJC" FT /db_xref="PDB:2KEI" FT /db_xref="PDB:2KEJ" FT /db_xref="PDB:2KEK" FT /db_xref="PDB:2P9H" FT /db_xref="PDB:2PAF" FT /db_xref="PDB:2PE5" FT /db_xref="PDB:3EDC" 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 // |
The output is to the specified graphics device.
The results can be output in one of several formats by using the command-line qualifier -graph xxx, where 'xxx' is replaced by the name of the required device. Support depends on the availability of third-party software packages.
The device names that output to a file are: ps (postscript), cps (colourps), png, gif, pdf, svg, hpgl, hp7470, hp7580, das, data.
The other available device names are: meta, x11 (xwindows), tek (tek4107t), tekt (tektronix), xterm, text.
Output can be turned off by specifying none (null).
See: http://emboss.sf.net/docs/themes/GraphicsDevices.html for further information on supported devices.
Program name | Description |
---|---|
dotmatcher | Draw a threshold dotplot of two sequences |
dotpath | Draw a non-overlapping wordmatch dotplot of two sequences |
polydot | Draw dotplots for all-against-all comparison of a sequence set |
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.
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.