Designs Highly Specific Oligos for MLPA® Assays
MLPA® Designer automates the design of highly specific synthetic oligos for MLPA assays. MLPA® (Multiplex Ligation dependent Probe Amplification) is a simple, high throughput multiplex PCR technique introduced by MRC-Holland that allows detection of abnormal copy numbers of up to 50 different genomic DNA or RNA sequences. This easy to perform technique requires the use of a thermocycler and capillary electrophoresis equipment. MLPA® Designer strictly adheres to the guidelines laid by MRC-Holland for designing of MLPA® oligos.
Data & Database Management
You can organize data of multiple experiments by creating separate projects for each of them. This functionality helps you to maintain a local database for sequence information and search results. There is no limitation to the number of projects that you can create using the program.
Avoid Cross Homologies- For Specific Oligo Design
Oligos binding to regions of the sequence other that the target leads to mispriming and false positive signals. To avoid this, MLPA® Designer interprets the BLAST search results and avoids the regions that have significant homologies with the database sequence. You can directly BLAST search from the program itself, and hence you do not need to go to the NCBI BLAST site, thereby saving time. We recommended that you run a BLAST search prior to performing a probe search to increase their specificity of the designed oligos. You can set the genome category against which you would like to BLAST search your target sequence, E value of the matches (by default, it is set to 1), whether or not you would like to apply filters to the query sequence (to mask repeats and low complexity regions) and the format of the output report.
Verify Specificity of MLPA® Oligo Design
You can BLAST search the designed probes against the genomic databases available at NCBI to verify the specificity of the design. In the report generated, the Score and E value of the significant hits are reported.
Multiplex MLPA® Oligos
The oligos designed for multiple sequences can be checked for cross-dimers with each other and with all the designed oligos, preventing competition in multiplex reactions. The free energies of the most stable cross dimers formed between the oligos designed for all the selected sequences are displayed by the program. This helps you to determine the degree of competition among the designed oligos in multiplex reactions.