title: Improved detection of DNA motifs using a self-organized clustering of familial binding profiles.
abstract: BACKGROUND
  One of the limiting factors in deciphering transcriptional regulatory networks is the effectiveness of motif-finding software. An emerging avenue for improving motif-finding accuracy aims to incorporate generalized binding constraints of related transcription factors (TFs), named familial binding profiles (FBPs), as priors in motif identification methods. A motif-finder can thus be 'biased' towards finding motifs from a particular TF family. However, current motif-finders allow only a single FBP to be used as a prior in a given motif-finding run. In addition, current FBP construction methods are based on manual clustering of position specific scoring matrices (PSSMs) according to the known structural properties of the TF proteins. Manual clustering assumes that the binding preferences of structurally similar TFs will also be similar. This assumption is not true, at least not for some TF families. Automatic PSSM clustering methods are thus required for augmenting the usefulness of FBPs.
  
  
  RESULTS
  A novel method is developed for automatic clustering of PSSM models. The resulting FBPs are incorporated into the SOMBRERO motif-finder, significantly improving its performance when finding motifs related to those that have been incorporated. SOMBRERO is thus the only existing de novo motif-finder that can incorporate knowledge of all known PSSMs in a given motif-finding run.
  
  
  BACKGROUND
  The methods outlined will be incorporated into the next release of SOMBRERO, which is available from http://bioinf.nuigalway.ie/sombrero
authors.affiliation: National Centre for Biomedical Engineering Science, NUI Galway Galway, Ireland. shaun.mahony@nuigalway.ie
authors.forename: Shaun
authors.initials: S
authors.lastname: Mahony
authors.forename: Aaron
authors.initials: A
authors.lastname: Golden
authors.forename: Terry J
authors.initials: TJ
authors.lastname: Smith
authors.forename: Panayiotis V
authors.initials: PV
authors.lastname: Benos
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D004330:Drosophila; D005656:Fungal Proteins / Q000737:chemistry; D020407:Internet; D015233:Models, Statistical; D009415:Nerve Net; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D005656:Fungal Proteins; D004247:DNA