The Bioinformatics Roadshow aims to address the needs of
European scientists for hands-on bioinformatics training. It is funded by
the European Commission as part of the FELICS Integrated Infrastructure
Initiative. The Bioinformatics Roadshow is coordinated by the European
Bioinformatics Institute – Europe’s main provider of biological data – and
is run in collaboration with our FELICS partners, the Swiss Institute of
Bioinformatics (SIB), the European Patent Office and the BRENDA project.
I will review basics of protein structure prediction, focusing on comparison of “physics-based” and “evolution-based” approaches. I will also introduce the GeneSilico TOOLKIT (available at https://genesilico.pl/toolkit/), a suite of tools for protein structural bioinformatics, available as an integrated web server. TOOLKIT it provides a ‘one stop shop’ for researchers interested in predicting protein tertiary structure from sequence and in accurate estimation to which extent the structural models can be trusted. During the lecture the entire pipeline will be described, the most important features will be highlighted, and the utility of TOOLKIT will be illustrated with practical examples.
Evolutionary basis of the theory of the
phylogenetic analysis is presented along with the specific
terminology applied in phylogeny reconstruction. The most
important data sources for phylogenetic analyses will be
presented with special emphasis on sequence data (DNA,
proteins). Three main algorithmic approaches to building of
phylogenetic trees will be shown: distance methods, maximum
parsimony, and likelihood methods. Methods of statistical
testing of phylogenetic results and for studying parallel
evolutionary events in cophylogenetic analysis in host-parasite
systems will be presented. An overview of the phylogenetic
software will be done along with the slideshow simulation of the
phylogeny reconstruction and statistic analysis of results.
The lecture and tutorial will give an overview over the current
state-of-the-art in RNA secondary structure. The lecture will start by introducing
the types of interaction in RNA, and their energetic contributions to RNA folding.
This model is then shown to allow the prediction of secondary structures, and several current
approaches will be explained. In particular, the Vienna Package, Mfold, Sfold, and methods for
pseudoknot prediction will be presented. The utility and limitations of typical input and output
formats will be discussed.
The main topic of the lecture will be structural and functional genome analysis. We will discuss issues related to genome sequencing, assembly and annotation. Lecture will start with sequencing technology, sequence data quality control, and tools for contamination removal. Next we will talk about sequence assembly challenges of genomes annotation: similarity, ab initio and combined methods for gene and regulatory regions prediction. These topics will be followed by the comparative genomics approaches to genomes analysis and pursue with some aspects of functional annotation: sequence based function prediction, motif based annotations, gene ontology. At the end we will discuss gene expression studies using EST and SAGE data.
|Polish Bioinformatics Society|