SoftBerry

Download bioinformatics toolbox release 2.3
includes pipelines constructing and running for Windows, Linux and MacOS platforms

Download selected software (New)

Run ReadsMap, Assembling, Genome alignments (synteny), Fgenesb_Annotator and Transomics pipelines on line.

CASE STUDIES:

Annotation of animal genomes: genes, promoters, functional motifs, protein sub-cellular localization: Softbery software, solutions and services.
Annotation of plant genomes: genes, promoters, functional motifs, protein sub-cellular localization: Softbery software, solutions and services.
Annotation of Bacterial Genomes and Community Sequences: Genes,
Operons, Promoters, Terminators, Protein Sub-Cellular Localization.
Analyze RNASeq Next Generation Sequencing Data:
- Accurate alignment of high-throughput RNA-seq data to a reference genome (ReadsMap);
- De novo transcriptome reads assembly into RNA transcripts (TransSeq);
Transomics - pipeline to map RNAseq data, assemble them into transcripts and quantify the abundance of these transcripts in particular datasets.
Analyze Genomic Next Generation Sequencing Data:
- De novo reconstruction (assembling) of genomic sequence,
- Reconstruction of sequences using reference genome,
- Mutation profiling and SNP discovery (OligoZip Assembler);
- Functional analysis of SNP (SNP-effect);

December 24, 2012. Softberry provided download about 100 software applications for free usage in research academic project. The download WEB page can be viewed here.

October 28, 2011. Softberry announces 11th release of RegSite database of plant regulatory elements. A list of its 2,252 entries representing 2,286 motifs can be viewed here.

>All news...

Automatic genome annotation Eukaryotic: animal, plant, fungi Bacterial and bacterial community DNA Visualization of annotations Genome Explorer Visualization of Bacterial genome comparison and annotation		Sequence comparison Alignment of genomic sequences Multiple alignment and tree construction Fast search in genomes ESTs clustering and visualization
Analysis of Gene Regulation Promoter prediction for animal and plant genes Search for functional motifs and conserved motifs Regsite database of regulatory motifs		Protein 3D-structure analysis and modeling Assignment of secondary structure and accesibility Alignments of 3D structures Restoring coordinates of side chains Prediction of secondary structures Fold recognition Homology modeling
Analysis of Expression data Clustering of co-expressed genes Finding disease/tissue/ condition specific gene sets		Analysis of protein functions Search for functional motifs Prediction of protein localization in cell Identification of SS-bonded Cys Prediction of protein disordered regions