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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




Softberry works in close contact with its clients and collaborators to meet all their computational genomics needs. Our team of researchers and software developers is able to solve most complex problems related to our area of expertise. The follwoing is the list of some services we perform for pharmaceutical and biotech companies.

Genome Annotation

We provide custom genome annotation services using our unique set of genome analysis tools. Typical annotation process involves the following steps:

  • Train parameters of gene-prediction programs on known genes of given organisms
  • Whenever practical, learning set is expanded to include genes of related organisms
  • Train and test parameters and select those optimal for the organism under analysis
  • Predict genes
  • Find exons similar to known proteins and ESTs and use this information to improve the accuracy of ab-initio gene prediction
  • Use our genome comparison tool to find conserved regulatory regions and further improve gene identification using sequences of related organisms
  • Define secondary strucure, functional site signature and cell location of predicted proteins.

Training parameters of gene-prediction programs

We develop for our clients custom-made data sets for gene- or functional site-prediction programs. These data sets can include known genes of given organisms, genes of related organisms, subsets of genes with particular expression patterns and other considerations.

Expression data analysis

Our GeneExplorer program reads and analyzes expression data represented by relative intensities of signals for different types of gene expression experiments. It can analyze all or marked groups of genes or tissues, select tissue-specific genes based on complex criteria, provide visual represenation of expression data, identify genes correlatively expressed in a given set of tissues, select disease-specific genes with particular characteristics, such as receptors or secreted proteins.

Customizing our software

We customize our software to meet needs of our clients: support of different computer platforms, modification of data formats for easy integration into customers' databases, development of databases with specific information compiled from public sources or computed from avaiable informaton. In addition, almost all our software is available with source codes, and therefore can be easily changed by customers themselves.

Custom Software Development

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