Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data

BMC Bioinformatics

Volumn 16, Issue 1, 2015, Pages

  Eggeling, Ralf ^a,b   Roos, Teemu ^b   Myllymäki, Petri ^b   Grosse, Ivo ^a,c  

^a MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^b UNIVERSITY OF HELSINKI   (Finland)

^c GERMAN CENTRE FOR INTEGRATIVE BIODIVERSITY RESEARCH IDIV HALLE JENA LEIPZIG   (Germany)

Author keywords

ChIP seq data; De novo motif discovery; Intra motif dependencies; Model selection; Transcription factor binding sites

Indexed keywords

LEARNING ALGORITHMS; MARKOV PROCESSES; NUCLEOTIDES; PULSE WIDTH MODULATION; STOCHASTIC MODELS; STOCHASTIC SYSTEMS; TRANSCRIPTION; TRANSCRIPTION FACTORS;

CHIP-SEQ DATA; INTRA-MOTIF DEPENDENCIES; MODEL SELECTION; MOTIF DISCOVERY; TRANSCRIPTION FACTOR BINDING SITES;

BINDING SITES;

DNA; PROTEIN BINDING; TRANSCRIPTION FACTOR;

ALGORITHM; BINDING SITE; BIOLOGY; CHEMISTRY; CHROMATIN IMMUNOPRECIPITATION; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METABOLISM; NUCLEOTIDE MOTIF; POSITION WEIGHT MATRIX; PROCEDURES; THEORETICAL MODEL;

ALGORITHMS; BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL BIOLOGY; DNA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MODELS, THEORETICAL; NUCLEOTIDE MOTIFS; POSITION-SPECIFIC SCORING MATRICES; PROTEIN BINDING; TRANSCRIPTION FACTORS;

EID: 84946557208     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0797-4     Document Type: Article

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