I have a list of primers for sequencing fungal ITS1/2 regions. I also have access to different fungal databases. I would like to perform in silico PCR analysis for comparing different primer pairs and choose the best one, which means, greater taxa amplification and the greater quantity of unique amplicons.
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$\begingroup$ Welcome to the site. Could you provide more details? What information is available on those fungal databases (maybe a link will help people) ? Do you have the identifiers of the primers or the full sequence of each primer ? Also, what have you looked up or what have you tried (we don't want to suggest things you already did: it is a waste of time for everybody) ? $\endgroup$– llrsApr 12, 2018 at 10:21
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$\begingroup$ The databases have the sequences (FASTA format) of the phylogenetic markers (named as ITS in fungi). One example of a database is UNITE (unite.ut.ee/repository.php). I have the full sequence of each primer, and I already try to use PrimerProspector software, but I'm new in this field of informatics, and I couldn't get this software to work. I had problems with previous versions of the programs required for PrimeProspector to work. Thanks for helping! $\endgroup$– bsmodaApr 13, 2018 at 14:24
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$\begingroup$ You should edit the new information into the question. Also what do you mean by "I couldn't get this software to work"? What are the messages you get? Note that this might be for another question but you seem to have a direction that is blocked, first try to solve this block if it helps to advance $\endgroup$– llrsApr 13, 2018 at 15:11
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