In-Silico PCR specifications


Unique identifier OMICS_02344
Name In-Silico PCR
Interface Web user interface
Restrictions to use None
Output data A file containing all sequence in the database that lie between and include the primer pair.
Output format FASTA
Computer skills Basic
Stability Stable
Maintained Yes



  • person_outline UCSC Genome Informatics Group <>
  • person_outline Jim Kent <>

In-Silico PCR citations

PMCID: 4014442

[…] primer pairs were designed from coding-exon sequences (cds) using primer3 [100] (opt. amplicon 200 bp, primer 18–25 bp, opt. tm 60°c, max. δtm 1°c, min. gc clamp 2 bp, max. homopolymer 3 bp). in silico pcr screening via e-pcr [101] required ≤1 amplicon (10 bp to 10 kbp) versus genome assembly and cds sequences. quantitative pcr was performed with 2 technical replicates and 3 biological […]

PMCID: 3742662

[…] 2step rt-pcr kit (qiagen, uk). all primers for this analysis were designed using the primer3 software (, and then they were blast searched against ucsc human. in-silico pcr tools. an aliquot of total rna from 48 samples, originating from four brain regions (occipital cortex, substantia nigra, medulla and cerebellum) and 12 individuals were used as a subset […]

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