FRAMA: from RNA-seq data to annotated mRNA assemblies

BMC Genomics
Martin BensKarol Szafranski

Abstract

Advances in second-generation sequencing of RNA made a near-complete characterization of transcriptomes affordable. However, the reconstruction of full-length mRNAs via de novo RNA-seq assembly is still difficult due to the complexity of eukaryote transcriptomes with highly similar paralogs and multiple alternative splice variants. Here, we present FRAMA, a genome-independent annotation tool for de novo mRNA assemblies that addresses several post-assembly tasks, such as reduction of contig redundancy, ortholog assignment, correction of misassembled transcripts, scaffolding of fragmented transcripts and coding sequence identification. We applied FRAMA to assemble and annotate the transcriptome of the naked mole-rat and assess the quality of the obtained compilation of transcripts with the aid of publicy available naked mole-rat gene annotations. Based on a de novo transcriptome assembly (Trinity), FRAMA annotated 21,984 naked mole-rat mRNAs (12,100 full-length CDSs), corresponding to 16,887 genes. The scaffolding of 3488 genes increased the median sequence information 1.27-fold. In total, FRAMA detected and corrected 4774 misassembled genes, which were predominantly caused by fusion of genes. A comparison with three different so...Continue Reading

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Datasets Mentioned

BETA
PRJNA68323
PRJNA283581

Methods Mentioned

BETA
RNA-seq
NMR
Chips

Software Mentioned

TGICL
EMBOSS GETORF
TCUR
Linux
Trinity
BLASTP
CLUSTALW
TFRAMA
STAR
CASAVA

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