MSRE-HTPrimer: a high-throughput and genome-wide primer design pipeline optimized for epigenetic research

Clinical Epigenetics

Table 3 Comparison of various features of MSRE-HTPrimer and other tools for primer design

Features	MSRE-HTPrimer v1.0	Primer Express v3.0.1	Primer Select	Primer Premier	Perl Primer v1.1.21	PRIMEGENS-v2.0	BiSearch
Genome-wide primer design	Yes	No	No	Yes	No	No	No
Dependency	No	Yes	Yes	Yes	Yes	Yes	Yes
Installation required	No	Yes	Yes	Yes	Yes	Yes	No
Operating system	All Unix, MAC, Windows	Windows	–	Windows, MAC	All Unix, MAC, Windows	All Unix, Windows	Web
Genome coordinate information^a	Yes	No	No	No	No	No	No
SNP annotation^a	Yes	No	No	Yes	No	No	No
Repeat element annotation^a	Yes	No	No	Yes	No	No	No
CpG Islands annotation^a	Yes	No	No	No	Yes	No	No
RefSeq gene annotation^a	Yes	No	No	Yes	No	No	No
Restriction enzyme type-II cut sites identification^a	Yes	No	No	No	No	No	No
Multi-processing capability	Yes	Yes	No	Yes	No	Yes	No
Multiple target sequences	Yes	Yes	No	Yes	No	Yes	No
Target sequence number restriction^a	No	Yes	Yes	Yes	Yes	Yes	Yes
Target sequence length restriction^a	No	Yes	Yes	Yes	Yes	Yes	Yes
FASTA sequence selection by tool	Yes	No	No	Yes	Yes	No	No
Custom primer selection quality matrix^a	Yes	No	No	No	No	No	No
Input file limitations	No	No	No	No	No	No	No
UCSC genome browser visualization^a	Yes	No	No	No	No	No	No
UCSC In-Silico primer design page cross-link	Yes	No	No	No	No	No	No
Availability	Free	Commercial	Commercial	Commercial	Free	Free	Free