SoftBerry

Download bioinformatics toolbox (New Version)
Comprehensive Desktop software package

Welcome to Softberry. Our scientific team is dedicated to developing and improving bioinformatics software to help identify genes and functional signals, determine gene function, decipher gene expression data and select disease-specific genes and drug target candidates. We are providing customized solutions to analyze and compare genomes, predict and annotate their genes based on sequence and structure comparison, recognition of conserved regulatory elements and defining cell location of predicted proteins.

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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

June 30, 2006. MolQuest ver. 1.4 is released, which includes 19 new programs for DNA, RNA and protein sequence analysis and five graphical tools for visualization of programs output. Trial version of Molquest for Windows can be downloaded here.

March 21, 2006. Softberry releases two protein 3D structure analysis programs. 3D-Match aligns 3D structures of two proteins, while 3D-MatchDB performs fast search of nonredundant PDB for structural homology with a query protein. Both programs can be tried here

December 20, 2005. Fourth release of RegSite database of plant regulatory motifs is now available. RegSite V.4 contains 1009 entries and more descriptive fields than other plant motifs databases. A list of RegSite entries is available here. To search for plant functional motifs from updated RegSite DB using NSITE-PL program, click here.

February 18, 2005. Softberry releases genefinding parameters for 240 prokaryotic genomes, including 25 archaea. Parameters are available for use with FGENESB bacterial gene and operon finding program here. Besides genome-specific parameters, they include generic eubacterial, archaea and mixed eubacterial-archaea parameters suitable for analysis of bacterial communities.

February 11, 2005. Softberry releases genefinding parameters for chicken and Xenopus New parameters can be used with FGENESH, FEX and BESTORF (here) and FGENESH+, FGENESH_C and FGENESH-2 programs (here). The accuracy of new parameters with FGENESH is 95-97% on nucleotide level.

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