BEACON is a software tool that compares annotations of a particular genome from different Annotation Methods (AMs). It uses GenBank format as input and derives Extended Annotation (EA) along side listing original annotations from individual AMs.
Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission
SplicingViewer is an integrated tool which can detect the splice junctions based on known gene models, annotate the alternative splicing patterns based on the splice junctions, and visualize the patterns of alternative splicing events. In addition, as a viewer, SplicingViewer can also be used to display the RNA-Seq reads mapping results with high speed and lower memory spend.
Jannovar is a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides HGVS-compliant annotations for both for variants affecting coding sequences and splice junctions as well as UTR sequences and non-coding RNA transcripts. Jannovar can also perform family-based pedigree analysis with VCF files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data.