LVA genes

MAKER2 predicted genes


We have used MAKER2 pipeline to predict genes. There are 28,094 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).

We adjusted the Maker2 pipeline parameters to yield 28,094 protein coding gene models. Of these, 11,728 yielded reciprocal best BLAST matches to the S. purpuratus RNAseq gene predictions. Among the reciprocal best BLAST models 407 matched the 539 transcription factor models from S. purpuratus. The mean size of the predicted gene sequences was 342 bp and the maximum was 12, 662 bp. The percent similarity to the purple sea urchin genes was 18%.

LVA genes can be searched using our LVA Gene Search