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EMBOSS: equicktandem |
equicktandem is a simple program that looks for segments in which each base tends to match the base 'repeatsize' back, i.e. with an autocorrelation peak at 'repeatsize'. This can allow drift in the repeating sequence, i.e. it does not look for a consensus sequence for the whole repeat block (that is what etandem does). But it is much quicker than etandem. It does not account for gaps.
The score is +1 for a match to the corresponding base 'repeatsize' back and -1 for a mismatch.
% equicktandem Input sequence: embl:hhtetra Output file [hhtetra.qtan]: Maximum repeat size [600]: Threshold score [20]:
Mandatory qualifiers: [-sequence] sequence Sequence USA -maxrepeat integer Maximum repeat size -threshold integer Threshold score [-outfile] report (no help text) report value Optional qualifiers: (none) Advanced qualifiers: -origfile outfile Output file name 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 |
-maxrepeat | Maximum repeat size | Any integer value | 600 |
-threshold | Threshold score | Any integer value | 20 |
[-outfile] (Parameter 2) |
(no help text) report value | Report file | |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-origfile | Output file name | Output file | <sequence>.equicktandem |
The output is a standard EMBOSS report file.
The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq
See: http://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.
By default equicktandem writes a 'table' report file.
The output from the above example is:
######################################## # Program: equicktandem # Rundate: Thu Apr 11 13:28:55 2002 # Report_file: stdout ######################################## #======================================= # # Sequence: HHTETRA from: 1 to: 1272 # HitCount: 1 # # Threshold: 20 # Maxrepeat: 600 # #======================================= Start End Score Size Count 191 935 339 6 124 #--------------------------------------- #---------------------------------------
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.
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.