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- W2279893206 abstract "Protein-DNA interactions are indispensable players in the daily activities of cells. DNA-binding proteins regulate gene expression and are responsible of DNA replication, packaging, repair and recombination. Among them, transcription factors activate/repress gene transcription by binding to specific genomic sites. Hence, the characterization of transcription factor binding sites turns out to be crucial in order to understand gene regulation. In this context, the development of computational tools is foremost. Here, I show the prediction of redundant transcription factors in yeast using a combination of homology-based tools and protein-protein interactions. The approach was automated and incorporated into ModLink+, an online and user-friendly tool to infer the fold of remote homologs. Moreover, I describe split-statistical potentials for protein-DNA interactions. Finally, I present SHAITAN, a statistical/homology-based approach that can be used to both predict transcription factor binding sites and infer the more likely transcription factors to bind a DNA sequence of interest. Les interaccions proteina-ADN son indispensables en l’activitat diaria de les cel•lules. Les proteines que participen en aquestes interaccions s’encarreguen de la regulacio de l'expressio genica i son responsables de la replicacio, l'empaquetament, la reparacio i la recombinacio de l’ADN. Entre aquestes proteines, els factors de transcripcio activen/reprimeixen la transcripcio de gens mitjancant la unio a llocs especifics dins el genoma. Per tant, la caracteritzacio dels llocs d'unio dels diferents factors de transcripcio es crucial per tal d’entendre com funciona la regulacio genica. En aquest context, desenvolupar eines computacionals es importantissim. En aquesta tesi predict redundancia entre factors de transcripcio de llevat eines fent servir eines basades en homologia i interaccions proteina-proteina. Aquesta aproximacio va ser automatitzada i incorporada a ModLink+, una eina accessible des d’internet i facil d'usar per a inferir el plegament de proteines a partir d’homolegs remots. D'altra banda, descric potencials estadistics fraccionats per a interaccions proteina-ADN. Finalment presento SHAITAN, una aproximacio basada en homologia i potencials estadistics que pot ser utilitzada per a predir els llocs d'unio de factors de transcripcio aixi com per saber quins factors de transcripcio son mes probables que s’uneixin a una determinada sequencia d'ADN." @default.
- W2279893206 created "2016-06-24" @default.
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- W2279893206 date "2015-01-21" @default.
- W2279893206 modified "2023-09-23" @default.
- W2279893206 title "On the characterization of protein-DNA interactions using statistical potentials and protein-protein interactions" @default.
- W2279893206 hasPublicationYear "2015" @default.
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