TXGP ens63 reference
One of the most interesting questions we can ask with X. laevis genome would be how many genes it has. To construct gene models, we are mainly focusing on de novo transcriptome assembly approach with our RNA-seq data. However, de novo transcriptome assembly programs generate many '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 precisely, we would like to combine all transcripts candidates foe each gene together, 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
This figure shows total number of genes and transcripts in each organisms. The number on top of green bar means total number of transcripts, and the number on top of blue bar means total number of genes (based on EnsEMBL v.63 annotation). The number on top of cyan bar means the number of genes that contain only one transcript.
Clustering of transcripts