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

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

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 informationa Yes No No No No No No
SNP annotationa Yes No No Yes No No No
Repeat element annotationa Yes No No Yes No No No
CpG Islands annotationa Yes No No No Yes No No
RefSeq gene annotationa Yes No No Yes No No No
Restriction enzyme type-II cut sites identificationa 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 restrictiona No Yes Yes Yes Yes Yes Yes
Target sequence length restrictiona No Yes Yes Yes Yes Yes Yes
FASTA sequence selection by tool Yes No No Yes Yes No No
Custom primer selection quality matrixa Yes No No No No No No
Input file limitations No No No No No No No
UCSC genome browser visualizationa 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
  1. aDenotes the unique feature of MSRE-HTPrimer in comparison to the other tools