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EMBOSS: dotmatcher |
The two sequences are placed on the axes of a rectangular image and (subject to threshold conditions) 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.
dotmatcher uses a threshold to define whether a match is plotted (calculated from the substitution matrix). A window of specified length is moved up all possible diagonals and a score is calculated within each window for each position along the diagonals. The score is the sum of the comparisons of the two sequences using the given similarity matrix along the window. If the score is above the threshold, then a line is plotted on the image over the position of the window.
% dotmatcher sw:hba_human sw:hbb_humanclick here for result
Mandatory qualifiers (* if not always prompted): [-sequencea] sequence Sequence USA [-sequenceb] sequence Sequence USA * -graph graph Graph type * -outfile outfile Display as data Optional qualifiers: -windowsize integer window size over which to test threshhold -threshold float threshold -matrixfile matrix Matrix file Advanced qualifiers: -data bool Output the match data to a file instead of plotting it |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequencea] (Parameter 1) |
Sequence USA | Readable sequence | Required |
[-sequenceb] (Parameter 2) |
Sequence USA | Readable sequence | Required |
-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 | EMBOSS_GRAPHICS value, or x11 |
-outfile | Display as data | Output file | <sequence>.dotmatcher |
Optional qualifiers | Allowed values | Default | |
-windowsize | window size over which to test threshhold | Integer 3 or more | 10 |
-threshold | threshold | Number 0.000 or more | 17.0 |
-matrixfile | Matrix file | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAMAT for DNA |
Advanced qualifiers | Allowed values | Default | |
-data | Output the match data to a file instead of plotting it | Yes/No | No |
Program name | Description |
---|---|
antigenic | Finds antigenic sites in proteins |
chaos | Create a chaos game representation plot for a sequence |
cpgplot | Plot CpG rich areas |
cpgreport | Reports all CpG rich regions |
diffseq | Find differences (SNPs) between nearly identical sequences |
dotpath | Displays a non-overlapping wordmatch dotplot of two sequences |
dottup | Displays a wordmatch dotplot of two sequences |
einverted | Finds DNA inverted repeats |
equicktandem | Finds tandem repeats |
etandem | Looks for tandem repeats in a nucleotide sequence |
garnier | Predicts protein secondary structure |
helixturnhelix | Report nucleic acid binding motifs |
isochore | Plots isochores in large DNA sequences |
newcpgreport | Report CpG rich areas |
newcpgseek | Reports CpG rich regions |
oddcomp | Finds protein sequence regions with a biased composition |
palindrome | Looks for inverted repeats in a nucleotide sequence |
pepcoil | Predicts coiled coil regions |
polydot | Displays all-against-all dotplots of a set of sequences |
pscan | Scans proteins using PRINTS |
redata | Search REBASE for enzyme name, references, suppliers etc |
restrict | Finds restriction enzyme cleavage sites |
seqmatchall | Does an all-against-all comparison of a set of sequences |
showseq | Display a sequence with features, translation etc |
sigcleave | Reports protein signal cleavage sites |
silent | Silent mutation restriction enzyme scan |
stssearch | Searches a DNA database for matches with a set of STS primers |
supermatcher | Finds a match of a large sequence against one or more sequences |
tfscan | Scans DNA sequences for transcription factors |
tmap | Displays membrane spanning regions |
wordmatch | Finds all exact matches of a given size between 2 sequences |
This is really just the wordmatch method with a grahical output.
Completed 1st June 1999. Last modified 16th June 1999.