Pipeline for gene-specific SSR marker identification in de novo transcriptome assembly

Question

[nathashanaranpanawa]

Hi,

I am a novice in all things bioinformatics and I'm facing some questions with my De novo transcriptome assembly.

I have assembled and assessed the quality of the transcriptome so far. How do I find out a set of specific genes related to a particular function in the organism? My end goal is to develop SSR markers and design primers for the genes related to a certain pathway in the organism. Any suggestions as to how I may proceed? Are there any established pipelines to be followed?

P.S. I mined SSR markers for the assembled transcriptome in whole, but again, I need to filter SSR markers for specific genes only.

Thanks

Answer 1

[h.mon]

Download the genes belonging to the pathway of interest from some database (NCBI, KEGG, etc), preferably from a closely related species. Make a blast database of your transcriptome and blast those genes against it. Check for SSR markers on the transcripts that strong matches according to the blast searches.

[nathashanaranpanawa]

Thanks. I will try that. To add to that, what is the blast method I should use?