Hi,

the simplest one will be to align the gene and the splice variants and compare the organization of introns and exons among the candidates

Thank you Ajay Saini for the response.

I have already tried that, but how can we distinguish which are splice variants( as there are 5 different forms of splice variants)from the paralogs?

Do you have any known splice variants that you can use as a reference sequence? That would at least help put your reads into groupings by similarity.

Hi,

I guess you plant to cluster or associate particular splice variants with different paralogs (gene copies in a genome). It should be possible with a careful alignment with perfectly placed intron/exon boundaries. Further, a comparison of sequence variations of paralogs with different regions of the splice variants will allow you to assign these to different gene copies. A clustering after the alignment will help you to identify which are splice variants and which are paralogs. The splice variants will have perfect sequence with some missing or alternative exons/UTRs, whereas the paralogs may also have sequence variations. You may have to handle gaps carefully while generating the trees.