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gear-genomics / dicey

In-silico PCR, primer design and padlock design for in-situ sequencing
https://www.gear-genomics.com/
GNU General Public License v3.0
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Add option to provide fasta of sequences to hunt command #13

Open bricoletc opened 6 months ago

bricoletc commented 6 months ago

Hello! Thanks for this great tool.

I'm using dicey hunt to check for uniqueness of primers in my target genome, and would like to do it in routine on a set of sequences, instead of one by one - could you/we add this as an input CLI parameter?

Best, Brice

tobiasrausch commented 6 months ago

Hi Brice,

For primer searches we developed dicey search and the web application silica because this subcommand includes Tm calculations, primer hits and amplicon predictions and this tool accepts a multi-FASTA file. Why is that subcommand not applicable for you?

Best, Tobias

bricoletc commented 6 months ago

IIUC, running dicey search will both match primers to the genome, and attempt to find amplicons from primer pairs - right? I wasn't specific enough: here I'm actually working on a set of sequences (that I called 'primers') that I don't want to get amplicons for - I just want to know where they match in the genome. So I suppose running search is a bit wasteful in that sense; but I could just focus on the primers part of the JSON output of search?

bricoletc commented 6 months ago

Though because search can take a FASTA, I assume hunt could pretty easily too in theory!

tobiasrausch commented 6 months ago

Sure, I write that down as an enhancement for the future. Thanks for the suggestion!