You can import sequences directly into the program from dbSNP and Entrez. Besides, you can import sequences saved locally in FASTA format or as a UCSC File in the program, if you are working with unpublished results.
You can design MLPA® oligos for all the exons present in a target sequence. For example, if a template sequence has 5 exons, the program would design oligos for each of the exons. If the exon information is present in Entrez, it is automatically retrieved and read by the program. If the exon information is not present, it can be easily added in the program. This helps in detection of exon deletions/duplications in e.g. the human BRCA1, MSH2 and MLH1 genes; detection of trisomies such as Down syndrome etc.
Supports copy number probe design: It can design MLPA® probes for abnormal copy number detection. The probes are designed avoiding cross homologies, specified SNPs and repeats.
Supports SNP specific design: The program designs MLPA® oligos that are SNP specific. The probes are designed such that the mutation lies within the amplicon. The program automatically avoids regions of cross homology to ensure high specificity. This helps in distinguishing sequences differing in only a single nucleotide. For e.g. 3 vs. 2 copies of a given gene sequence in a DNA sample.
MLPA probes can now be tagged with Luminex® MagPlex TAGs. TAGs can be imported into the program using MS Excel file that contain TAG details and instrument compatibility. For MLPA probe design, MLPA Designer chooses the tags such that dimerization, both between the probe and tag and amongst the tagged probes, is minimized. This ensures that the tags do not fold back on the oligos to create hairpins that may interfere with the ligation reaction or misprime to other oligo set. A user can override the program's recommendation and select a tag that best meets their research needs.
MLPA® Designer calculates the Tm values of the designed oligos using the most trusted and accurate nearest neighbor thermodynamic theory using the highly accurate Santa Lucia values.
The program displays a graphical view of all possible secondary structures such as hairpins, repeats and runs of the designed oligos. This helps to ascertain suitability of the designed oligos for a particular MLPA® experiment.
It displays detailed properties of the designed MLPA® oligos such as position, length, Tm, GC%, Hairpin ΔG, run length, and repeats.
The designed oligo sets, along with their properties, can be exported in standard excel and other spreadsheet formats for ordering synthesis or sharing results with colleagues.
You can control the oligo design by specifying the design parameters. Here are a few examples:
1) For copy number probe design, you can specify the range of the target sequence for which you would like to design the oligos.
2) You can alter the default range for Tm value and GC% as per your oligo design requirements.
3) You can choose from several alternate designs presented by the program depending on your experimental needs.
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.
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.