Data analysis using Softberry, public or cleints’ own pipelines in AWS cloud. Adopting pipelines to run on cloud computer clusters.
Genome and transcripts assembling, Reads Mapping, Alternative transcripts (Transomics pipeline), Snp discovery and evaluation, visualization
Bacterial gene, promoters, terminators, operons identification, metagenomics, Fgnesb pipeline. Microbiome sequence analysis and annotation.
Gene identification, HMM Fgenesh gene finder and Fgenesh++ genome annotation pipeline, building gene models accounting RNASeq data, finding alternatively spliced isoforms, 329 custom made gene-finding parameters
Gene identification, Fgenesh gene finder and Fgenesh++ genome annotation pipeline, 42 custom made gene-finding parameters. Largest Plant Gene Regulatory Elements database RegSite (~ 3000 entries).
De novo finding regulatory motifs, search for non-random occurrence of functional motifs, plant and animal regulatory motifs datables, promoters and poly_A sites identification. Recognition of Promoters Using Convolutional Deep Learning Neural Networks (CNN).
Alignment of sequences and genomes, multiple alignments, computing synteny between genomes, alignment of RNA and proteins onto genomic sequence
Comparison of 3D proteins structures, finding functional sites and protein sub-cellular location, secondary structure prediction, protein structure, visualization, fold recognition, homology modeling, molecular docking, molecular mechanics and dynamics computations
RNA folding, finding palindrome, finding miRNA and their targets, search for bacterial terminators