Computational protocol: A de novo transcriptome of the noble scallop, Chlamys nobilis, focusing on mining transcripts for carotenoid-based coloration

Similar protocols

Protocol publication

[…] From public databases, we compiled a dataset of the 15 known gene involved in carotenoid deposition were collected (TableĀ ). The amino-acid sequences of the known carotenoid deposition genes, covering carotenoid absorption, transport and cleavage, were used to search (tBlastn) for homologues in 454-derived sequences. Those sequences with scores more than or equal to 100 and E values less than or equal to 1e-10 were clustered to develop unigenes, and all of the unigenes were considered as candidate transcripts. The resulting unigenes were in turn used to search the GenBank databases by BlastX to confirm their putative carotenoid-related functions. […]

Pipeline specifications

Software tools TBLASTN, BLASTX
Application Amino acid sequence alignment
Organisms Mimachlamys nobilis