primer design strategy of xbai restriction sites for multiplex pcr  (PrimerDesign Inc)

Journal: BMC Genomics

Article Title: The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity

doi: 10.1186/s12864-021-08149-1

Figure Lengend Snippet: Comparison of different primer design software programs

Article Snippet: More importantly, multiplex PCR primer design software that can eliminate nonspecific amplification of the whole genome in multiplex PCR is rare and usually requires strenuous experimental validation.

Techniques: Comparison, Software, Multiplex Assay, Sequencing

Journal: BMC Genomics

Article Title: The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity

doi: 10.1186/s12864-021-08149-1

Figure Lengend Snippet: Multiplex PCR experimental process and sequencing results. A GT-seq experimental process. B Final library size. C The read coverage obtained with different primer concentrations. D Sequencing depth of targets

Article Snippet: More importantly, multiplex PCR primer design software that can eliminate nonspecific amplification of the whole genome in multiplex PCR is rare and usually requires strenuous experimental validation.

Techniques: Multiplex Assay, Sequencing

Journal: BMC Genomics

Article Title: The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity

doi: 10.1186/s12864-021-08149-1

Figure Lengend Snippet: Comparison of different primer design software programs

Article Snippet: Thus, a user-friendly, highly automated and highly user-defined web-based multiplex PCR primer design software is needed to minimize the work of primer design and experimental verification.

Techniques: Software, Multiplex Assay, Sequencing

Journal: BMC Genomics

Article Title: The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity

doi: 10.1186/s12864-021-08149-1

Figure Lengend Snippet: Multiplex PCR experimental process and sequencing results. A GT-seq experimental process. B Final library size. C The read coverage obtained with different primer concentrations. D Sequencing depth of targets

Article Snippet: Thus, a user-friendly, highly automated and highly user-defined web-based multiplex PCR primer design software is needed to minimize the work of primer design and experimental verification.

Techniques: Multiplex Assay, Sequencing

Journal: BMC Genomics

Article Title: The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity

doi: 10.1186/s12864-021-08149-1

Figure Lengend Snippet: Diagram of the Ultiplex workflow

Article Snippet: Here, we developed the web-based multiplex PCR primer design software “Ultiplex”.

Techniques:

Journal: BMC Genomics

Article Title: The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity

doi: 10.1186/s12864-021-08149-1

Figure Lengend Snippet: Filtration functions of Ultiplex. Primers need to be filtered with different functions to eliminate malfunctional pairs. A Getprimers.harpin_filter function. If there is a hairpin structure in the combined sequence of the primer and tag, the primer pair will be eliminated. B Getprimers.dimer_filter function. If there is a dimer structure between any two combined primer and tag sequences, the primer pair will be eliminated. C Getprimers.area_filter & Getprimers.site_filter functions. If any skipped sites or areas are located at the 3′ end of the primer, the primer pair will be eliminated. D Getprimers.single_blast_filter function. The potential binding sites of a single primer are evaluated, and if the amplicon length is below the cut-off value, the primer pair will be eliminated

Article Snippet: Here, we developed the web-based multiplex PCR primer design software “Ultiplex”.

Techniques: Filtration, Sequencing, Binding Assay, Amplification

Journal: Scientific Reports

Article Title: A new SNP genotyping technology Target SNP-seq and its application in genetic analysis of cucumber varieties

doi: 10.1038/s41598-020-62518-6

Figure Lengend Snippet: The procedure of target SNP-seq in genotyping 261 varieties with 163 perfect SNP. Library construction of target SNP-seq included two round of PCR. The first round of PCR was to capture the target SNP locus through multiplex PCR. The second round of PCR aimed to add a unique barcode adaptor for each DNA sample. Finally, the constructed library was sequenced on Highseq X platform.

Article Snippet: Finally, all perfect SNP loci were sent to the Molbreeding Biotechnology Company (Shijiazhuang, China) for multiplex PCR primer panel design.

Techniques: Multiplex Assay, Construct