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EMBOSS: etandem |
% etandem Input sequence: embl:hhtetra Output file [hhtetra.tan]: Minimum repeat size [10]: 6 Maximum repeat size [6]:
Mandatory qualifiers: [-sequence] sequence Sequence USA [-outfile] outfile Output file name -minrepeat integer Minimum repeat size -maxrepeat integer Maximum repeat size Optional qualifiers: (none) Advanced qualifiers: -threshold integer Threshold score -mismatch bool Allow N as a mismatch -uniform bool Allow uniform consensus |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence USA | Readable sequence | Required |
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.etandem |
-minrepeat | Minimum repeat size | Integer, 2 or higher | 10 |
-maxrepeat | Maximum repeat size | Integer, same as -minrepeat or higher | Same as -minrepeat |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-threshold | Threshold score | Any integer value | 20 |
-mismatch | Allow N as a mismatch | Yes/No | No |
-uniform | Allow uniform consensus | Yes/No | No |
The columns of the report show:
120 793 936 6 24 93.8 acccta 90 283 420 6 23 84.8 taaccc 38 432 485 6 9 90.7 ccctaa 26 494 529 6 6 94.4 ccctaa 24 568 597 6 5 100.0 aaccct
Program name | Description |
---|---|
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 |
isochore | Plots isochores in large DNA sequences |
newcpgreport | Report CpG rich areas |
newcpgseek | Reports CpG rich regions |
palindrome | Looks for inverted repeats in a nucleotide sequence |
polydot | Displays all-against-all dotplots of a set of sequences |
redata | Search REBASE for enzyme name, references, suppliers etc |
restrict | Finds restriction enzyme cleavage sites |
showseq | Display a sequence with features, translation etc |
silent | Silent mutation restriction enzyme scan |
tfscan | Scans DNA sequences for transcription factors |
This application was modified for inclusion in EMBOSS by Peter Rice (pmr@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.