In silico PCR tool

Virtual (in silico) or electronic PCR (ePCR) primers/probes or microRNA (miRNA) sequences search against whole genome (chromosome) prediction of likely PCR products and search for potential mismatches of the specified primers or probes. Search for multiple targets simultaneously within a specified range. In silico PCR primer searching is useful for the discovery of melting temperature target-binding sites.

An alternative command line Java application in silico PCR for local use without restrictions on genome size and the number of files to be analyzed.

Degenerate primer sequences are also accepted, each letter represents a combination of one or several nucleotides: B=(C,G,T), D=(A,G,T), H=(A,C,T), K=(G,T), M=(A,C), N=(A,C,G,T), R=(A,G), S=(G,C), V=(A,C,G), W=(A,T), Y=(C,T). U=Uracil, I=Inosine and LNA: dA=E, dC=F, dG=J, dT=L.

Input format: sequence can be pasted or uploaded as a file in FASTA format or retrieved sequence (NCBI’s accession, e.g. A02710) from NCBI’s "nuccore" nucleotide database.
Size Limitations: the length of the query sequence and the size of the batch file are theoretically unlimited.

Upload or paste sequence(s) in FASTA format:

Amplicon detection:		C>>T bisulfite conversion
Minimal amplicon size (bp):		Show all matching sites of primer binding
Maximal amplicon size (bp):		Show amplicon sequences
Mismatches allowed at the 3'-terminus:		Show only amplicons lengths

Run

Clear

To export the results: select all (Ctrl-A), copy (Ctrl-C) and paste (Ctrl-V).

С >> T bisulfite conversion (bisulfite modified genome)

Sequence, design of specific PCR primers for in silico bisulphite conversion for both strands - only cytosines not followed by guanidine (CpG methylation) will be replaced by thymines:

5’aaCGaagtCCCCa-3'        5’aaCGaagtTTTTa-3'
  |||||||||||||     ->      ||||||:|::::| 
3’ttGCttCaggggt-5'        3’ttGCttTaggggt