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Fig. 3 | Clinical Epigenetics

Fig. 3

From: MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics

Fig. 3

The MSP-HTPrimer web interface and output. a Web interface of MSP-HTPrimer query page. The query interface for MSP-HTPrimer shows different parameters that can be used to design and select optimized PCR primers for BSP [default option], MSP, COBRA, and MSRE assays; b an example of primer pair summary output table for MSP-PCR in MSP-HTPrimer web interface (for MSP primers two rows with alternate colors are displayed in light red color and light blue color backgrounds are for methylated and unmethylated primer pairs, respectively. The primer summary table contains target sequence ID, forward and reverse primer sequence, amplicon coordinates in BED format, hyperlink to visualize in UCSC genome browser, and in silico PCR database; and c an example output of the MSP-HTPrimer primer pair visualization in UCSC genome browser along with genomic (RefSeq, CpG islands, SNPs, and repeats) track within in BSP-HTPrimer web interface (For MSP primer, two tracks are displayed [red color for methylated primers and blue color for unmethylated primer]. Each result of the primer design pipeline is presented bundled, once as single red line [full amplicon] and as a line emphasizing forward and reverse primer below)

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