Data format example:
The following example is what generated the logos above. You can use upper
case letters as well as lower case letters. The first line indicate
basepairings. You can use letters and numbers, and the following type of
bracketts:
"(,)"; "[,]"; "{,}"; "<,>".
So the two first b's can for example be replaced with two "(", and the two
last b's with two ")". The data illustrated here is from Tuerk
et. al. PNAS 89, pp 6988-6992, 1992. Note that when having branching
configurations like
"((((....))))..((((....))))",
that these should be written such that the two stems are denoted with
different set of labels, for example as
"((((....))))..aaaa....aaaa".
If you only want to make a plain sequence logo you can just make the first
line consist of dots only.
> bb....aaaa....bb.....aaaa
> CCAGAGGCCCAACUGGUAAACGGGC
> CCG-AAGCUCAACGGGAUAAUGAGC
> CCG-AAGCCGAACGGGAAAACCGGC
> CC-CAAGCGC-AGGGGAGAA-GCGC
> CCG-ACGCCA-ACGGGAGAA-UGGC
> CCGUUUUCAG-UCGGGAAAAACUGA
> CCGUUACUCC-UCGGGAUAAAGGAG
> CCGUAAGAGG-ACGGGAUAAACCUC
> CCG-UAGGAG-GCGGGAUAU-CUCC
> CCG--UGCCG-GCGGGAUAU-CGGC
> CCG-AACUCG-ACGGGAUAA-CGAG
> CCG--ACUCG--CGGGAUAA-CGAG
Last updated September 19, 1997 by Jan Gorodkin
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