TXGP ens63 reference
One of the most interesting questions we can ask with X. laevis genome would be how many genes this frog have. To construct gene models, we are mainly focusing on de novo transcriptome assembly approach with our RNA-seq data, by using velvet+oases. However, many de novo transcriptome assembly program generates 'false positive' transcripts. Also, because of allotetraploidy in X. laevis, transcriptome data may contain many transcript variants for each gene. So, to estimate the gene model from transcriptome data, it would be helpful to combine all transcripts derived from the same gene, and analyze them separately. Sequence-based clustering is natural way to do this, but we need to optimize parameters, such as %identity to define a cluster.
To get some ideas for this, we have looked at genes and transcripts of several well-studied organisms.
Genes & Transcripts
= Clustering of transcripts to gene