footprint-discovery
Detect phylogenetic footprints by applying dyad-analysis in promoters
of a set of orthologous genes.
Adapted from the procedure described in Janky & van Helden (2008).
rekins@\bigre.ulb.ac.be
jacques.van.helden@\ulb.ac.be
The program takes as input a taxon of interest + one or several query
genes.
The output consists in a set of files, containing the results of the
different steps of the analysis.
- [prefix]_log.txt
-
Log file listing the analysis parameters + output file names;
- [prefix]_query_genes.tab
-
List of query genes (one or several genes can be entered)
- [prefix]_ortho_bbh.tab
-
List of orthologous genes
- [prefix]_ortho_seq.fasta
-
Promotoer sequences of the orthologous genes
- [prefix]_ortho_seq_purged.fasta
-
Purged promoter sequences (for motif discovery)
- [prefix]_filter_dyads.tab
-
Dyads found in the query genes (for dyad filtering)
- [prefix]_ortho_dyads.tab
-
Significant dyads found in the promoters of orthologous genes
(the footprints)
- [prefix]_ortho_dyads.asmb
-
Assembled dyads
- [prefix]_ortho_dyads.png
-
Feature-map
Use promoters of predicted operon leader genes
Infer operons in order to retrieve the promoters of the predicted
operon leader genes rather than those located immediately upstream of
the orthologs.
- Background model
-
Allow the user to choose among alternative background model (see Janky
& van Helden, 2008).
- taxfreq
-
Taxon-wide background model, computed by counting dyad frequencies in
all the promoters of all the genes of the reference taxon.
- monad
-
Expected dyad frequencies are the product of monad frequencies
observed in the input sequences.
- Dyads filtering
-
Only accept dyads found in the promoter of the query gene, in the
query organism.
- retrieve-seq
- get-orthologs
- dyad-analysis
Janky R, van Helden J (2008). Evaluation of phylogenetic footprint
discovery for the prediction of bacterial cis-regulatory elements. BMC
Bioinformatics, in press.