Toucan protocols

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Toucan specifications

Information


Unique identifier OMICS_06282
Name Toucan
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained No

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Publications for Toucan

Toucan in pipelines

 (3)
2013
PMCID: 3905855
PMID: 24038359
DOI: 10.1093/nar/gkt821

[…] element annotation system (ceas) server at http://ceas.cbi.pku.edu.cn (). the localization of e2f and cre motifs in e2f2-bound promoters was carried out with the motiflocator tool of the toucan program (). cutoffs of 0.85 and 0.9 and the ‘mouse 1 kb proximal 1000 ensmusg ()’ background were used. the modulesearcher tool of the toucan program was used to analyze promoter sequences […]

2012
PMCID: 3438128
PMID: 22852874
DOI: 10.1186/1471-2229-12-125

[…] retained to identify putative orthologs. promoter sequences (−1000 bps) were extracted from plant genomes with sufficient sequence coverage. auxres, zres and mres were mapped and illustrated using toucan 2 []. the gh3 protein sequences which were obtained from their corresponding cdna sequences were used for subsequent phylogenetic analysis applying the clustalw2 software at the embl-ebi […]

2011
PMCID: 3215682
PMID: 22004418
DOI: 10.1186/1471-2148-11-304

[…] 5s region. searches were performed within the first 78-120 nt upstream and downstream of the dna transcribing region. some putative 5s rdna transcriptional regulatory motifs were identified by the toucan workbench [] establishing a comparison with reference sequences from the drosophila eukaryotic promoter (epd) and jaspar database, and others were manually compared with published regulatory […]

Toucan in publications

 (15)
PMCID: 4777525
PMID: 26938778
DOI: 10.1371/journal.pbio.1002364

[…] total score and free energy. see for further information., to analyse and predict potential stat1, irf1 and irf9 binding sites in the promoter of human and mouse evl/evl, the open source software toucan was used []. see for further information., bmdm were treated with ifn-γ (10 u/ml) for 2, 6, and 24 h, fixed and then chromatin immunoprecipitation (chip) was performed as described previously […]

PMCID: 4330702
PMID: 25741346
DOI: 10.3389/fpls.2015.00029

[…] core set of cytokinin-induced genes were downloaded from tair using the bulk data retrieval tool (http://www.arabidopsis.org/tools/bulk/sequences/index.jsp). motif mapping was carried out using the toucan2 suite of sequence analysis tools (https://gbiomed.kuleuven.be/apps/lcb/toucan/toucan.jnlp) (aerts et al., , ). degenerated motifs were counted with the help of a self-made program written […]

PMCID: 3949115
PMID: 24653728
DOI: 10.3389/fpls.2014.00070

[…] positively to meja treatment. the subset of negatively responding pdf1s was not considered as it just involved a single sequence. searches for cis-regulatory motifs were conducted using the toucan workbench (aerts et al., ). with the toucan graphical interface, motifscanner software (aerts et al., ) was used to search for known regulatory elements stored in plantcare (lescot et al., ). […]

PMCID: 3681798
PMID: 23785430
DOI: 10.1371/journal.pone.0065498

[…] sites, using weight matrices from jaspar or transfac. (ii) it extracts significant clusters (region of the input sequences associated with a factor) by calculating a score function. the web tool toucan uses the motifscanner algorithm to search for potential tfbs in a set of sequences using the transfac or jaspar vertebrate databases. the information obtained from the motifscanner […]

PMCID: 3575264
PMID: 23324119
DOI: 10.1186/1471-2164-14-13

[…] stated otherwise, we define cis regions to our module genes as being 200 bp downstream and 1,000 bp upstream of the start of exon 1. the sequence data for these motif analyses was obtained via toucan [,], from the ensembl database. sequences corresponding to genes on reverse strand were reverse complimented., the putative roles of overrepresented sequence motifs, found by meme, […]

Toucan institution(s)
Laboratory of Neurogenetics, Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and K.U.Leuven Belgium; Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium; Human Genome Laboratory, Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and K.U.Leuven Belgium; Center for Biomolecular Medicine and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University Vienna, and Biomolecular Therapeutics Vienna, Austria
Toucan funding source(s)
This work is partially supported by Instituut voor de aanmoediging van Innovatie door Wetenschap en Technologie in Vlaanderen (IWT) (STWW-00162, STWW-Genprom, GBOU-SQUAD-20160), Research Council KULeuven (GOA Mefisto-666, GOA-Ambiorics, IDO genetic networks), FWO (G.0115.01 and G.0413.03) and IUAP V-22.

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