Concepts and introduction to RNA bioinformatics

TY - JOUR

T1 - Concepts and introduction to RNA bioinformatics

AU - Gorodkin, Jan

AU - Hofacker, Ivo L.

AU - Ruzzo, Walter L.

PY - 2014

Y1 - 2014

N2 - RNA bioinformatics and computational RNA biology have emerged from implementing methods for predicting the secondary structure of single sequences. The field has evolved to exploit multiple sequences to take evolutionary information into account, such as compensating (and structure preserving) base changes. These methods have been developed further and applied for computational screens of genomic sequence. Furthermore, a number of additional directions have emerged. These include methods to search for RNA 3D structure, RNA-RNA interactions, and design of interfering RNAs (RNAi) as well as methods for interactions between RNA and proteins.Here, we introduce the basic concepts of predicting RNA secondary structure relevant to the further analyses of RNA sequences. We also provide pointers to methods addressing various aspects of RNA bioinformatics and computational RNA biology.

AB - RNA bioinformatics and computational RNA biology have emerged from implementing methods for predicting the secondary structure of single sequences. The field has evolved to exploit multiple sequences to take evolutionary information into account, such as compensating (and structure preserving) base changes. These methods have been developed further and applied for computational screens of genomic sequence. Furthermore, a number of additional directions have emerged. These include methods to search for RNA 3D structure, RNA-RNA interactions, and design of interfering RNAs (RNAi) as well as methods for interactions between RNA and proteins.Here, we introduce the basic concepts of predicting RNA secondary structure relevant to the further analyses of RNA sequences. We also provide pointers to methods addressing various aspects of RNA bioinformatics and computational RNA biology.

KW - Algorithms

KW - Computational Biology

KW - Nucleic Acid Conformation

KW - RNA

KW - RNA Folding

U2 - 10.1007/978-1-62703-709-9_1

DO - 10.1007/978-1-62703-709-9_1

M3 - Journal article

C2 - 24639152

SN - 1064-3745

VL - 1097

SP - 1

EP - 31

JO - Methods in Molecular Biology

JF - Methods in Molecular Biology

ER -