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

 

 

Services for Universities and Academia

Academia

Softberry, Inc. is a leading developer of software tools for genomic and proteomic research.

There are several ways our academic customers use Softberry's software and expertise:

  • Licensing our popular programs, such as genefinders and EST_MAPping programs to support genome sequencing projects (Washington University Genomic Center, The Institute for Genomic Research (TIGR), Cold Spring Harbor Laboratory, Rutgers University and others)
  • Developing custom gene finding parameters for more accurate annotation of newly sequenced genomes (for example, Magnaporthe grisea for MIT/Whitehead Institute - follow the link for useful new genome annotation protocol using Softberry gene finders and customparameters)
  • Installation of entire program package for local network or web site use by students and scientists at the institution (Royal Holloway College of London University, Stowers Institute for Biomedical Research)
  • Collaboration in research and data analysis (Lawrence Berkeley National Laboratory, Royal Holloway College of London University)
  • Providing our data, such as annotations for eukaryotic and prokaryotic genomes, for databases and web informational resources (University of California at Santa Cruz).

Softberry's main areas of software development and expertise are:

  • Genome annotation and gene finding in eukaryotes, bacteria and viruses, EST mapping
  • Functional site identification in DNA and proteins, promoter finding
  • Genome comparison, fast genome and database search, and development of cross-platform interfaces for presentation of results
  • Expression data analysis
  • Protein structure prediction
  • Protein compartment (destination) prediction
  • EST clustering
  • Integration of genomic and expression data in cross-platform Java-based graphical interface.

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