Silica: in-silico PCR amplification

Input
Settings
Results
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Paste primers in Fasta format

or upload Fasta file (.fa)

and select genome

Maximum Size of PCR Product (bp)

Minimal Primer Tm to Consider (°C)

Number of bp from the 3' End of the Primer Used to Seach for Matches (>14)

Maximal Allowed Number of Mutations in Matching Sequence (0 or 1)

Keep Only PCR Products with Penalty Below (-1 = keep all)

Penalty Factor for Single Primer Tm Mismatch to optimal Tm

Penalty Factor for Tm Mismatch of Primers in a Pair

Penalty Factor for PCR Product Length

Tm Calculation: Concentration of Monovalent Ions (mMol)

Tm Calculation: Concentration of Divalent Ions (mMol)

Tm Calculation: Concentration of Annealing(!) Oligos (nMol)

Tm Calculation: Concentration of the Sum of All dNTPs (mMol)

Load JSON file (.json)

Application Description

Silica runs a virtual insilico PCR with a set of primers on a selected genome. Multiple primer pairs are allowed, off target products will be shown if present. All primer combinations are tested, provided sufficiend binding to the DNA and reasonable amplicon size.

Accepted Input

Primers can be provided in fasta format or uploaded as a fasta file (*.fa).

Sample Data

The "Load Example" button loads an example primer set. Hit "Launch Analysis" to try the functionality.

Output

Silica reports how many amplicons and primer binding sites were found. Results are shown in two tabs: The Amplicons tab with one entry per PCR product showing genomic location, length, penalty score, forward/reverse primer names, sequences, and Tm values and the Primers tab with one entry per binding site showing location and strand, primer sequence, matched genome sequence and Tm. Each entry includes a link to view the region in the UCSC Genome Browser (when available), and both tables can be downloaded as TSV files.