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Toggle navigation Softberry Run Programs Online Gene finding in Eukaryota Gene finding with similarity Operon and Gene Finding in Bacteria Gene Finding in Viral Genomes Next Generation Alignment (sequences and genomes) Genome visualization tools Search for promoters/functional motifs Deep Learning Recognition Protein Location RNA structures Protein structure Pathway prediction Protein/DNA 3D-Visual Works Manipulations with sequences Multiple alignments Synteny from genome contigs Analysis of gene expression data Plant Promoter Database Repeats SNP Proteomics Gene identification pipelines SpliceDB Computational methods to empower basic and applied research Next generation sequencing Annotation of Bacterial Genomes Annotation of Animal Genomes Annotation of Plant Genomes Alignment and Genome comparison Protein structure and functions RNA structure and functions Databases About Downloads Products Services In publications Leadership Contacts Cloud computing services Data analysis using Softberry, public or cleints’ own pipelines in AWS cloud. Adopting pipelines to run on cloud computer clusters. Next generation Genome and transcripts assembling, Reads Mapping, Alternative transcripts (Transomics pipeline), Snp discovery and evaluation, visualization Annotation of Bacterial Genomes Bacterial gene, promoters, terminators, operons identification, metagenomics, Fgnesb pipeline. Microbiome sequence analysis and annotation. Annotation of Animal Genomes 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 Annotation of Plant Genomes 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). Genome regulation analysis 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 and Genome comparison Alignment of sequences and genomes, multiple alignments, computing synteny between genomes, alignment of RNA and proteins onto genomic sequence Protein structure and functions 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 structure and functions RNA folding, finding palindrome, finding miRNA and their targets, search for bacterial terminators Copyright © 2020 www.softberry.com Internal page...