I am currently working on designing SSR primers for garlic and I'm planning to use EST sequences. I have downloaded ESTs from NCBI's GenBank (though, been trying the garlicdb website but to no luck, I cannot connect to it). Now, my problem is on how to deal with those sequences. I have read several publications on EST-based SSR markers where they directly search for SSRs and then design primers based on the search. While there are also publications where they assemble the ESTs into unigenes or contigs prior to SSR search and primer design.
So, what is the best way to design SSR primers from garlic EST data? Also, could anyone refer a good software to do the contig assembly? I have tried DNA Dragon by Sequentix and, I must say, it is good. However, there is no available citation for the said program. Anyone knows a good FREE program that could assemble contigs? I also have Staden pack (Gap4), but it's quite painful to convert 10k+ of sequences into individual staden files. So, I'm not using it until I am left with no further options.
Thank you in advance!
If your are up to use the EST dataset in database, you can use MISA software.
Thank you for the reply. I will look into those software and website.
You can also try NCBI dataset,you will get the primers for SSR markers for garlic.
Hi!!
1. It is best to assemble ESTs to obtain longer and unique sequences. It will also improve ur primer designing and functional annotation.
2. CLCgenomics workbench (trial for 14 days). Its interactive and easy.
3. Batchprimer3 is easy for multiple SSR primer designing.
Dear Grace, you can try this online resource to make your own SSR primers. http://archive.gramene.org/db/markers/ssrtool
It is very good tool to identify the all possible SSR in a given genomic DNA sequence as per various criteria defined by you. Once you identify SSR, then you can use any of the online primer finder tools to make SSR primers. All the very best.
You can generate long unigene assemblies from of EST sequences through use of CAP3 programme. Then use MISA program for SSR detection and primer designing.
You can directly generate SSRs from EST sequences through MISA.
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