de novo exon-exon junction identification tool from transcriptome assembly

Question

[hamzakhanvit]

Hi,

Are there any tools out there to find exon-exon junctions in transcriptome assembly contigs for non-model organisms which lack a reference genome?

Thanks, H

Answer 1

[mbens]

You could align your contigs to the genome sequence of a closely related species to identify exon boundaries. There are a variety of spliced aligners available and were compared for instance in

Iwata H, Gotoh O. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. Nucleic Acids Research. 2012;40(20):e161. doi:10.1093/nar/gks708. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488211/

Another approach could use information from orthologs. JuncDB lists intron positions in transcript alignments. You could add orthologous contigs to these alignments and identify probable exon boundaries.