Hmm, I'm not sure there's an easy way to do that. Even the Arabidopsis website is very focused on just the COL ecotype. If you can find a BLAST searchable database for all ecotypes that might be a workaround. Hopefully someone knows about a website/database that will have what you need.

Thanks for your response. I have found the genomic sequence of different ecotypes from 1001 Genomes, found the SNPs in the coding regions of my gene of interest from all ecotypes. But I need the amino acid sequences of the gene from all ecotypes. Lets see if I can figure it out.

There are some great peptide prediction programs. I like the Translate tool on ExPASy. It's user friendly and ignores gaps/numbers, input can be DNA or RNA, just google search these terms

Expasy - Translate tool

Dear Amy Klocko

Thank you for helping me. The problem is I am finding Arabidopsis ecotype sequence data from a Genome sequence project, hence those genes contain Intron regions and many 'NNNNNNNN' regions also, although I checked most of them are in the Intron regions only. Are there any tools which can predict Arabidopsis cds from DNA sequence? I found a few tools when googled it, but not convenient for Batch work and not getting the output files, only they are marking those regions. Manually I ned to splice them which is risky for more than 1000 sequences.

hmm, there must be a bioinformatics program that can do this sort of task. Got any bioinformatics folks in your department?

I guess you know the 1001genomes.org/tools.html webpage. There may be tools regarding your question. Otherwise, those people may be the right addressees to pose your question, and get a satisfying answer. Best wishes, Tony Schaeffner

This may not be what you're looking for, but could be helpful. 1001 proteome (https://www.heazleome.org/tools.html) tool has been discontinued, but you can use it as part of the ePlant website (https://bar.utoronto.ca/eplant/).