SMILE is a tool that infers motifs in a set of sequences, according to some criterias. It was first made to infer exceptionnal sites as binding sites in DNA sequences. Since the 1.4 version, it allows to infer motifs written on any alphabet (even degenerate) in any kind of sequences.
The specificity of SMILE is to allow to deal with what we call "structured motifs", which are motifs associated by some distance constraints. In particular, SMILE is able to group under a unique model different occurrences composed of several boxes separated by spacers of different lengths.
You'll find some algorithmic details in our publications.
SMILE is written in C/Unix. It exists a Debian package made an maintained by Steffen Möller (thanks a lot to him). To use it, just add
An on-line and simplified version is also vailable at Bioweb
(Pasteur Institute) (thanks to Catherine Letondal for her help).
Explanations and examples are given in the man page and the doc files of these packages.
A new tool, created by Alexandra M. Carvalho during her PhD, now makes the same job than SMILE, faster and more powerfull: RISO.
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