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EMBOSS: polydot |
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.
polydot compares all sequences in a set of sequences, draws a dotplot for each pair of sequences by marking where words (tuples) of a specified length have an exact match in both sequences and optionally reports all identical matches to feature files.
% polydot globin.fasta -gtitle="Polydot of globin.fasta"click here for result
Mandatory qualifiers:
[-sequences] seqset File containing a sequence alignment
-wordsize integer Word size
-graph graph Graph type
Optional qualifiers:
-[no]boxit bool Draw a box around each dotplot
-dumpfeat bool Dump all matches as feature files
-format string format to Dump out as
-ext string Extension for feature file
Advanced qualifiers:
-gap integer This specifies the size of the gap that is
used to separate the individual dotplots in
the display. The size is measured in
residues, as displayed in the output.
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| Mandatory qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequences] (Parameter 1) |
File containing a sequence alignment | Readable sequences | Required |
| -wordsize | Word size | Integer 2 or more | 6 |
| -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 |
| Optional qualifiers | Allowed values | Default | |
| -[no]boxit | Draw a box around each dotplot | Yes/No | Yes |
| -dumpfeat | Dump all matches as feature files | Yes/No | No |
| -format | format to Dump out as | Any string is accepted | gff |
| -ext | Extension for feature file | Any string is accepted | gff |
| Advanced qualifiers | Allowed values | Default | |
| -gap | This specifies the size of the gap that is used to separate the individual dotplots in the display. The size is measured in residues, as displayed in the output. | Integer 0 or more | 10 |
| 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 |
| dotmatcher | Displays a thresholded dotplot of two 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 |
| 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 RE 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 |
Completed 2nd June 1999.