We have sequenced a wild rice genome. However, we can not used it for our research by bioinformatics. We want to know the evolutionary information of the MADS-BOX gene between the model rice genome from Genebank and our newly sequenced wild genome. The first problem is how to get all the MADS-box gene from the newly sequenced wild rice? Of course, the MADS-box gene of the model rice gneome from genebank can downloaded. But, the next work is how?
One option is to use exonerate to map the MADS-box proteins in genbank to the genome that you have:
/home/user/bin/exonerate --model protein2genome --refine FULL \ --alignmentwidth 200 --showalignment \ --query sequences_from_genbank.fasta \ --target newly_sequenced_genome_assembly.fasta
This question is too general. I think you'd start with reading papers about analyses of molecular evolution of gene family and see how they approached similar questions. Usually you'll begin with aligning the know MADS-box genes in your references, probably as well as many other sequenced plant genomes to get a very conserved MADS domain consensus and run a tBLASTn on your newly assembled genome and annotate from there.