The sequences of pre-compiled cis-element lists are stored in perl-compatible regular expression, to represent ambiguous sequence patterns. Results are also presented using this expression. Users should follow the syntax of this expression to define "user-defined candidate list".
Several examples:
See http://perldoc.perl.org/perlrequick.html to find out more about regular expression.
| Helix-turn-helix(HTH) | (CTAATTG){2,3} |
| BBR/BPC | ((GA)+|(TC)+) |
| RAV | CAACA[ACGT]*CACCTG |
We also tried to evaluate pairwise combinations of motifs in the preliminary candidate list, in consideration for possible protein-protein interactions of multiple transcription elements binding cis-elements, as previously illustrated by experimental evidence (Ulmasov et al., 1995; Ulmasov et al., 1999).
Currently this is achieved by generate "combined cis-element candidate list" from the preliminary candidate list. For example if the preliminary list consists of three candidates, "AACC", "ATAT", and "GCAT", then "AACC.*ATAT", "AACC.*GCAT", "ATAT.*GCAT", "ATAT.*AACC" etc. will be included in the combined cis-element candidate list. Complementary sequences are also took in consideration, and thus motifs such as "GGTT.*ATGC" will also be added to the combined list. The members of this list will be evaluated just like members of the original candidate list.
Users can try such analysis by clicking on "Yes" for "Do Combined motif analysis" option. Note that it would be quite time-consuming.
Otherwise, users should note that it is possible to express combinations of cis-element by using regular expression (see above).
Last Update: 30 Nov., 2007