How to predict protein domains from a list of mRNA sequences?

Question

[Min Dai]

I have a list of mRNA (mature mRNA) sequences. I performed the transcriptome assembly, so some of the mRNA sequences have not been annotated before.

My aim is to annotate domains for all the potential amino acid sequences from these mRNAs. Some obstacles exist:

• A de novo protein domain prediction tool is needed.
• One mRNA always has more than one open reading frame.

I am wondering whether there exists an integrated tool or website that can calculate all the potential domains when I just input the mRNA sequences.

Thank you in advance!

[h.mon]

Have a look at Trinotate and dammit, two annotation pipelines. See also

Domain Prediction Tool