A .pdf copy with 16 Pags.- Figs.- Tabls. from the original presentation by authors at Training Event.  Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0).Peer reviewe

Contreras-Moreira, Bruno

Sebastián Yagüe, Álvaro

van Helden, Jacques

Digital.CSIC

footprintDB & RSAT::Plants  RSAT mirror for plants integrated with DB of  transcription factors of known DNA motifs  B Contreras-Moreira, A Sebastián,  J van Helden  Estación Experimental de Aula Dei-CSIC ,Zaragoza, Spain Université d'Aix-Marseille, France      http://greekc.org/activity/lisbon-training-event                                                 Lisboa, 25/10/2017 2 Features of plant promoters  RSAT::Plants data sources other sources                  3              47               2                                                         + Compara   homologues                          + Gene  Ontology .dna.toplevel.fa .dna_rm.toplevel.fa .gtf .pep.all.fa Compara biomart 3 RSAT::Plants: assembled genome size Source: http://plants.rsat.eu/data/stats 4 RSAT::Plants stats: scaffold/contig size Source: http://plants.rsat.eu/data/stats 5 RSAT::Plants stats: upstream regions <1-2kb> Source: http://plants.rsat.eu/data/stats 6 Source: http://floresta.eead.csic.es/footprintdb LYS 46 ILE 47 ARG 5 GLN 50 ASN 51 MET 54 G C C A T T A G R K I Q N M …Rqtytryq…lslterqiKIwfQNrrM… 7 Protein-DNA complexes in the PDB help annotate TFs Contreras-Moreira B & Sebastian A(2016)  Methods in Molecular Biology, 1482:259-77 URL  8 Sample footprintDB entry Accessions:  VRN1 (EEADannot 20150505) Names:  BM5A, HvBM5A, Vernalization1, VRN-H1, VRN1 Organisms:  Hordeum vulgare cv Strider Libraries:  EEADannot 20150505 1 Notes:  family:MADS-box Length:  244 Pfam Domains:       9-59 SRF-type transcription factor (DNA-binding and dimerisation domain)    78-173 K-box region Sequence:      1 MGRGKVQLKRIENKINRQVTFSKRRSGLLKKAHEISVLCDAEVGLIIFSTKGKLYEFSTE   60   61 SCMDKILERYERYSYAEKVLVSSESEIQGNWCHEYRKLKAKVETIQKCQKHLMGEDLESL  120  121 NLKELQQLEQQLESSLKHIRARKNQLMHESISELQKKERSLQEENKVLQKELVEKQKAQA  180  181 AQQDQTQPQTSSSSSSFMMRDAPPVADTSNHPAAAGERAEDVAVQPQVPLRTALPLWMVS  240  241 HING Interface Residues:  3, 4, 15, 18, 19, 23, 159, 163 3D-footprint homologues:  1n6j_A, 1egw_B, 1hbx_D, 1mnm_A, 3a5t_B Source: http://floresta.eead.csic.es/footprintdb 9 cis-regulatory elements in footprintDB Source: http://floresta.eead.csic.es/footprintdb 10 Features of plant promoters  footprintDB benchmark Sebastian A & Contreras-Moreira B (2014) Bioinformatics 30(2):258-65 URL 0204060801001202 3 4 5 6 7 8 9 101112131415frequency length of cis elements  nr95 monomers (Jul2015) Contreras-Moreira B & Sebastian A(2016)  Methods in Molecular Biology, 1482:259-77 URL  11 1) interrogating footprintDB: web interface  Contreras-Moreira B & Sebastian A(2016)  Methods in Molecular Biology, 1482:259-77 URL  1.1) DNA Motif Search (register to save results) 1.2) Proteome-Specific DNA Search 12 1) interrogating footprintDB: web interface Contreras-Moreira B & Sebastian A(2016)  Methods in Molecular Biology, 1482:259-77 URL  1.3) Protein Sequence Search 13 2) interrogating footprintDB: SOAP web service Source: http://floresta.eead.csic.es/footprintdb/index.php?documentation https://bioinfoperl.blogspot.com.es/2017/10/soap-interface-of-footprintdb.html  14 3) interrogating footprintDB: aligning to FASTA peptides, BLASTP >1:ACE2 [Saccharomyces cerevisiae] libs:JASPAR;CISBP; motif:vTGCTGGtym;mCCAGCa; http://floresta.eead.csic.es/footprintdb/index.php?motif=cb6f6b343b895dfa1c3776c99fbedda7  MDNVVDPWYINPSGFAKDTQDEEYVQHHDNVNPTIPPPDNYILNNENDDGLDNLLGMDYYN IDDLLTQELRDLDIPLVPSPKTGDGSSDKKNIDRTWNLGDENNKVSHYSKKSMSSHKRGLS GTAIFGFLGHNKTLSISSLQQSILNMSKDPQPMELINELGNHNTVKNNNDDFDHIRENDGE NSYLS… Sources: http://floresta.eead.csic.es/footprintdb/download https://bioinfoperl.blogspot.com.es/2017/04/genome-annotation-with-footprintdb.html  3.1) all nr TFs 3.2) metazoa 3.3) plants 15 4) ways of interrogating footprintDB:  motif collection in RSAT Contreras-Moreira B, Castro-Mondragon J, Rioualen C, Cantalapiedra CP, van Helden J (2016)  Methods in Molecular Biology, 1482:279-95 URL Castro-Mondragon J, Rioualen C, Contreras-Moreira B, van Helden J (2016) Methods in Molecular Biology, 1482:297-322 URL Thanks!  http://eead.csic.es/compbio  

RSAT mirror for plants integrated with DB of transcription factors of known DNA motifs

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