The institute of Molecular Biology and Biotechnologies is offering to diverse clients to perform original and targeted LC-Mass based metabolomics analyses for different compounds in plants, animals and humans. The methods for plants are developed for the resurrection plant Haberlea rhodopensis Friv., where we have long lasting experience, and very successfully can be used for other plants with high burden of phenolic substances as well as for different agriculture plants. The IMBB also offers LC-Mass targeted investigations for biologically-active compounds in medical plants and high-value bioactive commodities (carotenoids, anthocyanes, flavonoids etc.) from agriculture plants.

Metagenomics:

The rapid evolution of all sequencing technologies (Next Generation Sequencing, or NGS), has revolutionized metagenomics analysis.

Modern Metagenomics constitutes a state-of-the-art approach aiming to investigate the metabolic potential of microbial communities and provide a better understanding of microbial ecology, dynamics and potential interactions. With massive amount of NGS data, Metagenomics analysis can reveal the structural and functional repertoire of microbial communities.

For the analysis of metagenomics data, we the following workflow:

• Data quality control – FastQC, Trimmomatic;
• Data assembly into contigs or scaffolds – MEGAHIT metaSPAdes, ABySS;
• Gene prediction and gene annotation – rpsBLAST;
• Taxonomic analysis – Mothur;
• Comparative analysis.

Additionally, we use automated pipelines such as web-based MG-RAST, MEGAN6 and GALAXY Metagenomics tools. We can provide graphical representation of the microbiome and metagenome.

Genome assembly:

Our bioinformatics department is offering several standard bioinformatics services, including NGS data preprocessing, Genome assembly, Genome annotation and Comparative genome analysis. Our team is also offering custom-tailored analyses.

We provide both De-novo and reference genome assembly for many small genomes such as plant, bacterial, bacteriophage, virus, and some fungal genomes. We use the software applications such as SPAdes, Abyss, and Velvet for the draft assembly of short reads. However, draft assemblies usually results in many gapped scaffold sequences. To remedy this, we apply automated strategies called SSPACE and GapFiller. These are reliable tools capable of closing gaps within scaffolds, using paired-reads. These methods show good results for both bacterial and eukaryotic datasets.

Delivered output:

• Raw data quality reports;
• Assembly summary report, containing results from genome assembly and quality statistics;
• Generated contigs and scaffolds in Fasta format;
• Bandage output files, visualizing de novo assembly graphs.

Genome annotation:

Genome annotation follows Genome assembly and describes individual genes and their products – RNA or proteins. We offer structural and functional genome annotation, encompassing the prediction of open reading frames (ORFs), gene structure (exon-intron structure), regulatory motifs, as well as assigning biological functions to these elements. This process involves both manual and automated annotation. We perform a search in multiple prominent databases such as KEGG, Uni-Prot/Swiss-Prot, GeneOnthology, etc. In addition, our service includes the widely used homology-searching programs BLAST and BLAST2Go, along with several Web-based annotating platforms such as DOGMA, Web Apollo, GenSAS, and RAST.

Delivered output:

• Annotated genes in GFF and GeneBank formats;
• Reports, containing a full annotation of coding sequence regions, tRNA and rRNA.

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 analysing 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 still 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 isforms, based on sequence overlap and a number of gap calculations.

IMBB offers also to perform:

• Metagenomics investigations (bioinformatics part).
• NGS sequencing investigations (bioinformatics part) of various genomes