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Gene finding
Gene finding with similarity
Gene finding in Bacteria
Gene finding in Viruses
Gene search
Gene explorer
Promoter
Protein location
RNA structure
Protein structure
3d-explorer
SeqMan
Multiple alignment
clust
Analysis of expression data
Human-Mouse Synteny
Plant promoter database
Search and map repeats
Extracting known SNPs

 

 

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Software SummarySoftware manualsApplied in Publications
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
Recent News

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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