SoftBerry

Download bioinformatics toolbox New release 2.3
includes pipelines constructing and running for Window and Linux (New) platforms

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.
A Tool for Reconstructing Sequences and Transcriptome analysis using New Generation Sequencing Technology Data

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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

October 14, 2009. Softberry announces a pipeline for assembly and analysis of transcriptome data obtained using next generation sequencing technologies. The pipeline can be used to estimate gene expression levels, identify alternative splice variants, and improve gene proediction and genome annotation using transcription data. More details are available here.

October 9, 2009. Release 7 of RegSite plant regulatory elements database is available. The release contains 1816 antries, a list of which can be seen here.

February 14, 2008. Softberry releases OligoZip package for analysis of Solexa/Illumina and similar sequencing reads. It can be used for genomic sequence assembly - de novo or based on a reference genome - and mutation profiling ans SNP discovery.

January 31, 2008. Softberry releases MolQuest 2.0 Alpha version, which supports user-customizable pipelines. Its trial version can be downloaded at www.molquest.com

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