The aim of these tutorials is to give a theoretical and practical
introduction to the Regulatory Sequence Analysis Tools
(RSAT) software suite. The most convenient way to follow the
tutorial is to display the current page in a separate window, and to
use the tools with the current one.
The RSAT home page displays two frames. The frame on the left contains
a menu, presenting the available tools. Each time you click on a tool
name, the right frame displays the form for the corresponding tool.
The tools are organized in a modular way : rather than having a single
form for the complete analysis, we found it more convenient to present
separate forms for the successive steps of a given analysis. A typical
analysis will thus consist in using successivbely different tools (for
example sequence retrieval -> motif discovery
-> pattern matching ->
feature-map). For this purpose, the tools are interconnected,
allowing you to send automatically the result of one request as input
for the next request (piping). The links between tools are illustrated
in the flow chart below. An advantage of this modular organization is
that you can either follow a full pipeline throught the tools, or
directly enter at any step of an analysis with external data of your
own.
We will analyze some practical examples to get familiar with the
different tools, and the way they are interconnected.
The tutorials contains different parts, illustrating the typical
situations that can be encountered when analysing regulatory sequences :
Pattern matching: you know the regulatory motif
(e.g. the consensus for a transcriptional factor), and you are
interested by one or several particular sequences (e.g. promoters of a
gene of interest, or binding fragments obtained from ChIP-on-chip
experiments): you look for the matching positions within the
sequences.
Genome-scale pattern matching: you know the regulatory
motif, and you would like to scan the genome to detect genes having
this motif in their regulatory regions, which may be considered as
potential target genes for the transcription factor of interest.
Motif discovery (or pattern discovery). You know
the sequences, you ignore the regulatory motif : you dispose of a set
of functionally related regulatory sequences (e.g. promoters of
co-expressed genes, or peaks collected from ChIP-seq experiments), and
you suspect that they are enriched in binding site for one or seveal
transcription factors. You thus want to detect a motif "ab
initio" from the sequences.
Detailed protocol for matrix-scan:
Turatsinze, J.V., Thomas-Chollier, M., Defrance, M. and van
Helden, J. (2008) Using RSAT to scan genome sequences for
transcription factor binding sites and cis-regulatory modules. Nat
Protoc, 3, 1578-1588.
Pubmed
18802439
oligo-analysis:
detection of over-represented oligonucleotides (words).
dyad-analysis:
detection of over-represented spaced pairs of oligonucleotides.
position-analysis:
detection of words having a positional bias in sequences aligned on
some reference position.
Detailed protocol for string-based motif discovery:
Defrance, M., Janky, R., Sand, O. and van Helden, J. (2008) Using RSAT
oligo-analysis and dyad-analysis tools to discover
regulatory signals in nucleic sequences. Nature Protocols 3,
1589-1603. Pubmed 18802440
plant upstream sequences: motif discovery on the Web browser or running a Docker container:
Ksouri N, Castro-Mondragón JA, Montardit-Tardá F, van Helden J, Contreras-Moreira B, Gogorcena Y (2021)
Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example.
Plant Physiol 185(3):1242-1258. Pubmed 33744946 (updates Pubmed 27557774)
