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Gene finding
Gene finding with similarity
Gene finding in Bacteria
Gene finding in Viruses
Next Generation
Gene search
Gene explorer
Protein location
RNA structure
Protein structure
Multiple alignment
Analysis of expression data
Plant promoter database
Search and map repeats
Extracting known SNPs



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



Recent News

August 10, 2013. Softberry developed genefinding parameters for 30 new genomes, for use with FGENESH suite of gene prediction programs on its own or in conjunction with Transomics pipeline, which uses next generation sequencing data analysis to discover alternative splice variants.

December 24, 2012. Softberry provides free download of about 100 genome and protein analysis programs for use in research academic research. Download page.

>All news...

Software SummarySoftware manualsApplied in Publications
Automatic genome   annotation
Eukaryotic: animal, plant, fungi
Bacterial and bacterial
  community DNA
Visualization of annotations
GenomeSeuqence Explorer
Visualization of Bacterial
   genome comparison
   and annotation

Sequence comparison
Alignment of genomic sequences
Multiple alignment and tree
Fast search in genomes
Analysis of Gene Regulation
Promoter prediction for
   animal and plant genes
Search for functional
   motifs and conserved motifs
Regsite database of regulatory
Protein 3D-structure analysis and modeling
Assignment of secondary structure and accesibility
Alignments of 3D structures
Restoring coordinates
   of side chains
Prediction of secondary
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
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