Bioinformatics:

The Center of Plant Systems Biology and Biotechnology (CPSBB) and the Institute of Molecular Biology and Biotechnologies (IMBB) offes to perform original and targeted bioinformatics analyses to diverse clients with following custom-developed software:

miRDEG:

miRDEG is a software package designed for the identification and discovery of putative novel miRNAs through the use miRNA biogenesis characteristics in sRNA sequencing data, combined with miRNA degradation product databases. The package is comprised of three separate software applications (cluster SD, miRNA2D, miCompare) and one standalone software module (LoopRNA). clusterSD focuses on the identification of sRNA clusters consistent with miRNA biogenesis and matching this against clusters of the expected degradation products of a mutative miRNA. miRNA2D focuses on analyzing the secondary structures of the RNA regions identified by clusterSD, looking for characteristic primary miRNA structures. miCompare focuses on verifying putative miRNAs against databases of known miRNAs in order to verify result viability.

LoopRNA:

LoopRNA is a Java module intended to aid in the design of software for RNA secondary structure analysis. By employing OOP and Graph theory, this module represents RNA secondary structure as a non-linear tree graph comprised of standalone, internally linked objects. This representation is considerably easier to examine via automated software while retaining a human-readable output option. LoopRNA is not a standalone programme, but rather a module intended for implementation in larger software applications. LoopRNA is not intended to visual, store or reinterpret RNA secondary structure data. Superior formats such as Vienna and RNAML already serve this purpose well. Rather, LoopRNA is intended to create a self-contained logical architecture where each element is “aware” of its own characteristics. This architecture can be polled for simple questions which would be trivial to answer by a human operator looking at a graphical visualisation, but which are tedious and complicated to code into software and which tend to be difficult to maintain as requirements change. In short, LoopRNA is intended to examine RNA secondary structure through software as a human operator can by eye.

Clustering Module:

Clustering Module is a precursor to the clusterSD software application in the miRDEG software package. It focuses on the identification of pairs of sRNA clusters in sequencing data, which are then matched against standard miRNA biogenesis characteristics. Specifically, the Clustering Module looks for sRNA which match the sequenced miRNA and miRNA* sequences, along with their isoforms, based on sequence overlap and a number of gap calculations.

The Center of Plant Systems Biology and Biotechnology (CPSBB) and the Institute of Molecular Biology and Biotechnologies (IMBB) offer to perform original and targeted metabolomics investigations: