equicktandem identifies regions in a nucleotide sequence which are likely to contain tanden repeats. For a region to be reported, it must be no larger than a specified maximum repeat size and must score higher than a threshold score, which is also user-specified. The output is a standard EMBOSS report file with details of the location and score of any potential tandem repeats. Optionally, the output can be written in the format of the Sanger Centre quicktandem program.
equicktandem looks for sequence segments in which each base tends to match the base a fixed number ('repeatsize') of nucleotides back in the sequence, i.e. with an autocorrelation peak at 'repeatsize'. The score for a segment is the sum of the scores for each position in that segment: the score is incremented (+1) for a match to the corresponding base 'repeatsize' back and decremented (-1) for a mismatch. The algorithm allows for drift in the repeating sequence, i.e. exact matches are not required, nor is a consensus sequence for the whole repeat block used (that is what etandem does). The algorithm does not account for gaps but it is much quicker than etandem.
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By default equicktandem writes a 'table' report file.
A tandem repeat in a DNA sequence is where a sequence of two or more nucleotides is repeated without any intervening nucleotides. For example "GATACAGATACAGATACA" is a tandem repeat of "GATACA". A short tandem repeat is typically 2 to 10 base pairs and occur in introns. The sequence and number of repeats at a given locus tend to be characteristic of an individual. Where enough STR loci are examined, a unique genetic profile of an individual can be built. Thus, tandem repeats are useful for genotyping, for example, in determining parentage and in forensic cases.
To identify genuine tandem repeats, the repeat sizes and / or sequence regions identified by equicktandem can be used as input to etandem. etandem will confirm which regions are true tandem repeats and give an accurate specification of the repeats.
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