Abstract：
:This protocol explains how to discover functional signals in genomic sequences by detecting over- or under-represented oligonucleotides (words) or spaced pairs thereof (dyads) with the Regulatory Sequence Analysis Tools (http://rsat.ulb.ac.be/rsat/). Two typical applications are presented: (i) predicting transcription factor-binding motifs in promoters of coregulated genes and (ii) discovering phylogenetic footprints in promoters of orthologous genes. The steps of this protocol include purging genomic sequences to discard redundant fragments, discovering over-represented patterns and assembling them to obtain degenerate motifs, scanning sequences and drawing feature maps. The main strength of the method is its statistical ground: the binomial significance provides an efficient control on the rate of false positives. In contrast with optimization-based pattern discovery algorithms, the method supports the detection of under- as well as over-represented motifs. Computation times vary from seconds (gene clusters) to minutes (whole genomes). The execution of the whole protocol should take approximately 1 h.
journal_name
Nat Protocjournal_title
Nature protocolsauthors
Defrance M,Janky R,Sand O,van Helden Jdoi
10.1038/nprot.2008.98subject
Has Abstractpub_date
2008-01-01 00:00:00pages
1589-603issue
10eissn
1754-2189issn
1750-2799pii
nprot.2008.98journal_volume
3pub_type
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