Probe Design only.

Probe design algorithm could be used to find sequence-specific probes, which doesn't show any blast hit against database. Such probe design has been used for targeted sequencing like agilent sure-select technology with next-generation sequencing.

Probe design algorithm uses, sliding window protocol to find fragment of user-given length. Also the algorithm could be used to design multiple probes scattered around query sequence to cover whole region.

To design gene specific probes, PRIMEGENSv2 uses sliding window protocol to find fragment of user-given length by the PRIMEGENSv2 variable PROBE_LENGTH as the window size. This sliding window moves over length of PROBE_PERIOD ('Probe shift' in Figure). It looks for probe in every next genomic region given by the PRIMEGENv2 parameter named as PROBE_REGION ('Inter-probe distance' in Figure). For probe design, user can also provide their preference of maximum and minimum GC content in the probe using PRIMEGENSv2 other variables as MAX_GC and Min_GC and maximum allowable BLAST hit for probes.

Probe Design figure