MAKER2 predicted genes
We have used MAKER2 pipeline to predict genes. There are 29,697 predicted genes. Briefly gene models were generated by masking all repeats, training set was generated using EST(isotigs) and protein evidence alignments to the genome(Scaffold) and finally genes were predicted using ab initio predictors(SNAP and augustus).
The parameters we used produced 29,697 protein coding gene predictions. Of these, 8,995 yielded a reciprocal best BLAST with the S. purpuratus RNAseq transcripts. Among these reciprocal best BLAST instances 376 matched the 539 annotated transcription factor models from S. purpuratus. The mean size of the gene models was 355 bp and ranged up to 7965 bp. The percent similarity compared to the sea urchin genes was a mean of 16% and ranged from 0.3 to 98%.
PMI genes can be searched using our PMI Gene Search