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

Table 1 Comparison of various features of MSP-HTPrimer and other tools for primer design

Features	MSP-HTPrimer v1.0	PrimerExpress v3.0.1	PrimerSelect	PrimerPremier	MethPrimer	PRIMEGENS-v2.0	BiSearch
Genome-wide primer design	Yes	No	No	Yes	No	No	No
Primer design on reverse strand^a	Yes	No	No	No	No	No	No
Dependency	No	Yes	Yes	Yes	No	Yes	Yes
Installation required	No	Yes	Yes	Yes	No	Yes	No
Operating system	Web-based	Windows	–	Windows, MAC	Web-based	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 island 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 site identification^a	Yes	No	No	No	Yes	No	No
Multiprocessing 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	No	No	No
Custom primer selection quality matrix^a	Yes	No	No	No	No	No	No
Input file limitations^a	No	Yes	Yes	Yes	Yes	Yes	Yes
UCSC genome browser visualization^a	Yes	No	No	No	No	No	No
Availability	Free	Commercial	Commercial	Commercial	Free	Free	Free

ISSN: 1868-7083