back and -1 for a mismatch.
Usage
Here is a sample session with equicktandem. The input sequence is the
human herpesvirus tandem repeat.
% equicktandem
Input sequence: embl:hhtetra
Output file [hhtetra.qtan]:
Maximum repeat size [600]:
Threshold score [20]:
Command line arguments
Mandatory qualifiers:
[-sequence] sequence Sequence USA
[-outfile] outfile Output file name
-maxrepeat integer Maximum repeat size
-threshold integer Threshold score
Optional qualifiers: (none)
Advanced qualifiers: (none)
General qualifiers:
-help bool report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
|
Mandatory qualifiers |
Allowed values |
Default |
[-sequence] (Parameter 1) |
Sequence USA |
Readable sequence |
Required |
[-outfile] (Parameter 2) |
Output file name |
Output file |
<sequence>.equicktandem |
-maxrepeat |
Maximum repeat size |
Any integer value |
600 |
-threshold |
Threshold score |
Any integer value |
20 |
Optional qualifiers |
Allowed values |
Default |
(none) |
Advanced qualifiers |
Allowed values |
Default |
(none) |
Input file format
The input for equicktandem is a nucleotide sequence
Output file format
The output from equicktandem is an uncommented list of identified repeats.
In a future version this will change to be annotated sequence features.
The columns of the report show:
- Score
- Start base position
- End base position
- Repeat size
- Repeat count
339 191 935 6 124
Data files
None.
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with a status of 0.
Known bugs
None.
Program name | Description |
einverted | Finds DNA inverted repeats |
etandem | Looks for tandem repeats in a nucleotide sequence |
palindrome | Looks for inverted repeats in a nucleotide sequence |
equicktandem identifies regions wich are likely to contain tanden
repeats. tandem should then be run on those regions to confirm
them and to get an accurate specification of the repeats. tandem
runs slowly.
Author(s)
This program was originally written by Richard Durbin at the Sanger Centre.
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.
History
Completed 25 May 1999
Target users
This program is intended to be used by everyone and everything,
from naive users to embedded scripts.
Comments