RNA motif discovery: a computational overview

BEAM web server: a tool for structural RNA motif discovery

Motivation RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure pr...

Introduction to Computational Biology Lecture # 10: Motif Discovery

In the previous lessons we learned about a probabilistic model which describes biological sequences Hidden Markov Model (HMM).We have also learnt how to evaluate the parameters of a specific HMMby an expectation-maximization algorithm (EM). In this lesson we will use these methods to solve the specific problem of motif discovery. Our goal is to find a word that appears in a non-conserved place ...

RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space.

Given the wealth of new RNA structures and the growing list of RNA functions in biology, it is of great interest to understand the repertoire of RNA folding motifs. The ability to identify new and known motifs within novel RNA structures, to compare tertiary structures with one another and to quantify the characteristics of a given RNA motif are major goals in the field of RNA research; however...

A Combined Motif Discovery Method

Computational Approaches for Drug Design and Discovery: An Overview

The process of drug discovery is very complex and requires an interdisciplinary effort to design effective and commercially feasible drugs. The objective of drug design is to find a chemical compound that can fit to a specific cavity on a protein target both geometrically and chemically. After passing the animal tests and human clinical trials, this compound becomes a drug available to patients...