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Question: The Methods To Determine Mads-Box Gene Families In A Newly Sequenced Genome? I Need The Information About The Gene Family Sequence Of Dna, Cdna, Location On Chrommone,Motif?
0
gravatar for Liu Tao
8.7 years ago by
Liu Tao • 0
Liu Tao • 0 wrote:

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?

genome sequence motif • 1.8k views
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modified 8.7 years ago by Arelicorlaior • 50 • written 8.7 years ago by Liu Tao • 0

For next time: "urgent" and "help" are not good or useful question tags.

ADD REPLY • link written 8.7 years ago by Neilfws ♦ 49k
2
gravatar for Arelicorlaior
8.7 years ago by
Arelicorlaior • 50
Arelicorlaior • 50 wrote:

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
ADD COMMENT • link written 8.7 years ago by Arelicorlaior • 50
1
gravatar for Vitis
8.7 years ago by
Vitis • 2.4k
New York
Vitis • 2.4k wrote:

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.
ADD COMMENT • link written 8.7 years ago by Vitis • 2.4k
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