In addition of screening the entire iGEM registry, we have developped a tool to help a biology iGEM team. This team is ________________________________. It consisted in finding the DNA sequence of the primer, given three input sequences: the two sequences that will undergo the PCR, and the complete resulting sequence.

The software will find 4 primers: the forward primer overlapping with the first input, the reverse user primer that overlaps with the first sequence and the gap sequence added on the PCR, the forward user sequence, overlapping with the second sequence and the gap sequence, and endly the reverse primer, which overlaps with the second sequence. If some suffix, prefix or terminator are added on the full sequence, they will be added in the forward and reverse primers. To detect the length of the overlapping part of the primers, we search for the correct length that will have the desired melting temperature. This melting temperature is calculated with the equation:

deltaH

Tm = ----------------------------------------- - 273.15 + 16.6log[Na+]

-10.8 + deltaS + Rln([oligo]/4)

with R = 1.987 cal/(mol K) Gas constant, [oligo] = 5E-07 M, [Na+] = 0.05 M. The find the position of the cutting enzyme (where the nucleotide U was placed), we search for an A in the gap sequence, and a matching T 8~13bp further. The A will be replaced by the U in the reverse user primer, and the T will be replace by the U in the forward user primer.

This tool will be useful also for biologist working on the VBI lab, as they had to do it manually before, and it was pretty slow and subject to human errors.

An executable with explanantions to use it (on windows or on linux) are available here:_________. This software can be used with the interface shown previously, or with command line only (to automatisized it easily). The input can be the 3 sequences or a file containing these 3 sequences. The source code of this software is also available ____________.