Построение оптимальных моделей ДНК-сайтов связывания факторов транскрипции высших эукариот на основе данных различных экспериментальных методов тема диссертации и автореферата по ВАК РФ 03.00.28, кандидат физико-математических наук Кулаковский, Иван Владимирович

• Кулаковский, Иван Владимирович
• кандидат физико-математических наук
• 2009

Оглавление диссертации кандидат физико-математических наук Кулаковский, Иван Владимирович

Введение.

Актуальность темы.

Цели и задачи исследования.

Научная новизна.

Практическое значение.

Апробация работы.

Заключение диссертации по теме «Биоинформатика», Кулаковский, Иван Владимирович

Выводы

1. Разработан метод построения оптимальной модели ССТФ с использованием экспериментальных данных, полученных традиционными экспериментальными методами. Метод реализован в виде вычислительного алгоритма Показано, что при использовании данных ДНК футпринтинга для построения мотивов, распознаваемых ССТФ, необходимо использовать участки генома, прилегающие к картированным футпринтам. Предложен алгоритм, реализующий учет информации, содержащейся в геномных фланках футпринтов, при построении ОБЛВ.

2. Разработан метод построения оптимальной модели ССТФ путем интеграции данных различных экспериментальных методов, включая современные высокопроизводительные техники на базе иммунопреципитации хроматина. Метод реализован в виде вычислительного алгоритма СЫршипк.

3. Создан набор программных средств, реализующих предложенные алгоритмы. Созданные программы позволяют на базе различных вычислительных платформ анализировать данные, полученные с использованием широкого спектра экспериментальных методик. Создан единый вычислительный конвейер, интегрирующий новые алгоритмы и существующие программные инструменты АЬоРго и 8е81МСМС.

4. Создана коллекция мотивов связывания факторов регуляции транскрипции ВгоБорЬИа те1апо^аз1ег, содержащая мотивы, полученные с использованием практически всей экспериментальной информации, представленной в открытых источниках. Показано, что разработанные методы позволяют выявить мотивы связывания, превосходящие по своим характеристикам известные мотивы связывания, для широкого набора белков-регуляторов транскрипции.

5. Разработанные программные средства и построенные коллекции уточненных мотивов доступны в сети Интернет по адресам: http://line.imb .ac.ru/DMMPMM, http://line.imb. ac.ru/iDMMPMM, http://line.imb.ac.ru/Chipmunk.

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