We have a set of probes for which we need to check if the probe has non-specific targets. But we need to search each probe against a large number of genomes. A large number of hits are coming up and it is very tedious to manually check each hit. Is there a way to make this faster and accurate?
Abhijeet Singh
Suppose, I want to identify a specific gene in a microorganism. I design probes that hybridize against the target. To check for non-specific hybridization, I do a BLAST search with the probe sequence against several genomes and get a large no. of hits. The process of validating each hit manually is a challenging task. So is there a way to make this more fast and accurate?
So, the simple aim is to get the name or taxonomy of the sequences to which the probe attach. This is fairly easily and can be done in multiple ways. Since there is no difference in primer/probe at the structural level, several primer utilities can be used. Blast could be an option but it would need to optimize the parameters to get meaningful hits.
I am not sure how you are carrying out the task, but if you are using the web-Blast, I have a way to suggest. If you are friend with CLI, there are many tools which can be modified to do the task.
Hi Arpit, You can install offline NCBI blast tools in your machine. Create the database of microgranisms which you want to check the specificity against your probes. Run the local blast in your machine for probes against this database. Check the output of blast results and select whatever hit you want. May be you can write simple script here in your preferred langauage to make it very quick to find the correct hit.
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