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.
• Analyze RNASeq Next Generation Sequencing Data:
  • Accurate alignment of high-throughput RNA-seq data to a reference genome (ReadsMap);
  • De novo transcriptome reads assembly into RNA transcripts (TransSeq);
• Transomics - pipeline to map RNAseq data, assemble them into transcripts and quantify the abundance of these transcripts in particular datasets.
• Analyze Genomic Next Generation Sequencing Data:
  • De novo reconstruction (assembling) of genomic sequence,
  • Reconstruction of sequences using reference genome,
  • Mutation profiling and SNP discovery (OligoZip Assembler);
  • Functional analysis of SNP (SNP-effect);

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.