Gemi: PCR Primers Prediction from Multiple Alignments

Table 1

Comparison between Gemi and other existing public tools.

Criteria	Gemi	Primer3	easyPAC
Simplicity	Yes	Yes	Yes
Fast^1	Yes	Yes	*
User friendly	Yes	Yes	Yes
Multiple and divergent sequences^2	Yes	NA	#
Long sequences^3	Yes	NA	*
Cross-platform	Yes	Online	Yes
Probes’ design	Yes	Yes	NA
GC content	Yes	Yes	Yes
Temperature	Td	Tm	Tm
Temperature range^4	Yes	NA	#
Hairpin structure	NA	Yes	#
Parameters^5	Basic	Advanced	Advanced

The table represents a comparison between Gemi, Primer3, and easyPAC tools. (Yes) denotes it is covered by the tool, (NA) means not offered by the tool, (*) means offered but Gemi performs better in this function, while (#) means this option is offered referring to the paper.
¹Gemi can retrieve primers and probes within seconds (Section  4 in supplementary document, SI-1). Primer3 searches for primers within short fragment of the sequence; its performance is relatively fast. EasyPAC performed slower than Gemi.
²Gemi succeeded to find primers and probes for multiple and divergent (aligned) sequences with about 30% identity, while Primer3 could not parse divergent sequences and easyPAC failed to retrieve any primer.
³Gemi successfully presented primers and probes for input sequences of about 10 kbp; the same process cannot be accomplished by Primer3 and easyPAC.
⁴In case of degenerate nucleotides in a position within primers, Gemi reports the temperature range of these nucleotides. Based on the paper, easyPAC reports it as well.
⁵Although Primer3 and easyPAC tools offer advanced functions, Gemi is designed to cover the basic needs of biomedical field to find reliable primers within minutes with user-friendly interface.