FRAMA

FRAMA (From RNA-seq to Annotated MRNA Assembly) is a software tool that annotates and refines de novo mRNA assemblies obtained from RNA-seq data. It addresses several post-assembly challenges in reconstructing full-length mRNAs, particularly in complex eukaryotic transcriptomes with similar paralogs and multiple alternative splice variants.

Key features and functionalities of FRAMA include:

1. Reduction of contig redundancy
2. Ortholog assignment
3. Correction of misassembled transcripts
4. Scaffolding of fragmented transcripts
5. Coding sequence identification

The authors applied FRAMA to assemble and annotate the transcriptome of the naked mole-rat. They assessed the quality of the obtained transcript compilation using publicly available naked mole-rat gene annotations. FRAMA annotated 21,984 naked mole-rat mRNAs (12,100 full-length CDSs), corresponding to 16,887 genes, and improved the median sequence information by 1.27-fold through the scaffolding of 3,488 genes. The tool also detected and corrected 4,774 misassembled genes, primarily caused by gene fusion.

Comparative analyses revealed that FRAMA's gene models are better supported by RNA-seq data than other naked mole-rat transcript sets.