FRAMA

FRAMA reconstructs and annotates de novo transcriptomes from second-generation RNA sequencing (RNA-seq) data to produce low-redundant, full-length mRNA and coding sequence catalogs for organisms lacking a reference genome, including resolution of paralogs and alternative splice variants.

Key Features:

• Genome-independent annotation: Operates without a reference genome, enabling annotation of organisms with incomplete or unavailable genomic data.
• Reduction of contig redundancy: Reduces redundancy among assembled contigs to produce a low-redundant transcript catalog.
• Ortholog assignment: Assigns orthology to assembled transcripts to facilitate comparative genomics.
• Correction of misassembled transcripts: Detects and corrects misassemblies, including those caused by gene fusion events.
• Scaffolding of fragmented transcripts: Scaffolds fragmented transcripts to extend sequences, increasing median sequence information (e.g., 1.27-fold increase observed in naked mole-rat).
• Coding sequence identification: Identifies coding sequences (CDSs) within assembled transcripts to annotate full-length CDSs.

Scientific Applications:

• Transcriptome assembly and annotation: Produces de novo transcriptome assemblies and annotations, as demonstrated for the naked mole-rat transcriptome.
• Gene expression studies: Generates high-quality gene models that support detailed gene expression analyses.
• Comparative transcriptomics: Supports comparative studies across species or conditions via orthology assignment and redundancy reduction.

Methodology:

Builds upon de novo assemblies generated by tools such as Trinity and applies post-assembly refinement tasks—including correction of misassemblies, scaffolding of transcripts, orthology assignment, redundancy reduction, and coding sequence identification—and was validated by annotating 21,984 mRNAs corresponding to 16,887 genes and correcting misassemblies in 4,774 genes in the naked mole-rat study.