Question: de novo exon-exon junction identification tool from transcriptome assembly
gravatar for hamzakhanvit
3.6 years ago by
hamzakhanvit10 wrote:


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

ADD COMMENTlink modified 2.1 years ago by mbens100 • written 3.6 years ago by hamzakhanvit10
gravatar for mbens
2.1 years ago by
mbens100 wrote:

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.

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.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by mbens100
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