MOUNT KISCO, N.Y.–(BUSINESS WIRE)–Softberry, Inc. announces release of a comprehensive set of biomedical research-oriented software applications for academic users to install and run locally on a limited basis.
The programs, already cited in thousands of scientific publications, are available for Linux and Mac OS platforms and focus primarily on genomic and proteomic research. They include tools for analysis of next generation sequencing data: Accurate spliced alignment of RNA-Seq data to a reference genome (ReadsMap), de novo assembly of transcriptome reads into RNA transcripts (TransSeq), genome assembly (OligoZip) and a software package for SNP analysis (SNP-Toolbox).
Another group of programs facilitates analysis of genomic sequences: alignment of genomes, bacterial and eukaryotic promoter prediction, discovery of functional/regulatory motifs, splice sites identification and gene prediction. EST_map and Prot_map programs, often used in genome annotation pipelines, map entire databases of known mRNA or protein sequences to genome.
Software for protein sequence and structure analysis includes tools for identification of sub-cellular protein location, prosite pattern search, 3D structure comparison, protein structure modeling using molecular dynamic approach and homology modeling.
There are also programs for RNA secondary structure prediction, search for miRNA sequences, and a suite of programs for analysis of expression data.
Software for general statistical data analysis includes Visan (visual analysis) package with discriminant analysis, neural networks and principal component modules.
A dozen of graphical viewers for visual and interactive analysis of sequences, structures, and outputs of many programs completes the collection of software free for academic use. The programs are available for download at www.softberry.com/downloads.
Most of the programs available for free download are also included in integrated environment of MolQuest bioinformatics software package that can be downloaded for free trial at www.molquest.com.
Softberry, Inc. is a leading developer of research oriented software tools for genomic and proteomic research. Among its customers are all five largest agribiotech companies, numerous academic and research institutions, such as JGI, JCVI, Washington University, UC Berkeley, and Cold Spring Harbor Laboratory, and several pharmaceutical and biotech companies. Softberry has about 20 employees and offices in Mount Kisco, NY and Novosibirsk, Russia. Additional information is available at www.softberry.com.