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多路连接依赖探针扩增（MLPA）检测拷贝数和突变检测
AlleleID是设计MLPA合成探针或者由MRC Holland引入的多重连接依赖探针扩增技术的程序，当合适的工具包不可用时，研究人员能够扩展这项技术。这是一种快速增长的高通量基因图谱分析方法。可以检测外显子缺失、拷贝数变化和CpG甲基化模式。具有成本效益合适、敏感性高、特好和可再生性好等特点。
AlleleID为PamGene检测设计了mRNA特,DNA特和突变特MLPA探针。这将使PamChip用户在使用PamGene高精度检测平台时设计自己感兴趣的基因探针检测。结合这两种技术，拷贝数的变化和突变可以很*地在6小时内检测到。
Taxa Specific/Cross Species Identification: Conserved Probe with Optimal Primers
Conserved Probe with Optimal Primers: AlleleID® designs a primer pair that would amplify the maximum number of sequences possible in an alignment. There are two choices available for designing primers, Unique and Optimal. For "Unique", the program designs a primer pair to amplify each sequence. Each primer is completely homologous to its template. For "Optimal', the program minimizes the number of primers required to amplify all sequences; taking advantage of the fact that primers can bind to a sequence and amplify it even if they contain a limited number of mismatched bases especially towards the 5' end of the primer.
AlleleID® Provides Several Design Options for Designing Taxa Specific/Cross Species Assay
Conserved Probes with Conserved Primers: AlleleID® identifies conserved regions by aligning sequences and then designs a probe within them. This enables identification of any sequence in the set with a single probe. It also designs primer pairs in the conserved regions flanking the probes. As a result, a single primer pair can amplify all the sequences of a group or a taxa.
When designing a taxa specific assay, AlleleID® designs a single common probe to identify a taxa or a group of organisms from the mix. For challenging problems when such designs are not feasible, AlleleID® attempts the design by minimizing mismatches, avoiding them especially towards the more problematic 3' end.
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