Fig. 2

The MSRE-HTPrimer web interface and output. a Web interface of MSRE-HTPrimer query page (the query interface for MSRE-HTPrimer shows different parameters that can be used to design and select optimized PCR primers for MSRE assay and genomic sequencing assay). b An example of primer pair summary output table in MSRE-HTPrimer web interface (an example of primer pair summary table for RefSeq Human gene MGMT [chr10: 129467190–129768042, RefSeq ID NM_002412.4]. It contains target sequence ID, forward and reverse primer sequence, amplicon coordinates in BED format, link to display and download to UCSC genome browser, and display to In-Silico PCR database). c An example output of the MSRE-HTPrimer primer pair visualization in UCSC genome browser along with genomic (MSRE cut sites, RefSeq, CpG islands, SNPs, and Repeats) track within MSRE-HTPrimer web interface (in order to focus and illustrate MSRE-HTPrimer features, all redundant UCSC genome browser tracks are hidden in 2C presenting from top to bottom; the MSRE cutsites position, the localization of RefSeq Human gene MGMT [chr10: 129467190–129768042, RefSeq ID NM_002412.4], CpG islands, simple nucleotide polymorphisms based on dbSNP 142 [rs18153536588 and rs16906252], and the kind of repeating elements [low complexity]. 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). d An example output of In-Silico PCR database search display of primer pairs (an example of primer pair display in UCSC In-Silico PCR database for RefSeq human gene MGMT [chr10: 129467190–129768042, RefSeq ID NM_002412.4])