Supporting information S1 Table Comparison of NGS-PrimerPlex and other tools functionality: a —choosing genome regions to amplify by gene names and their parts. XLSX Click here for additional data file. TIF Click here for additional data file. S3 Fig A Approach used by NGS-PrimerPlex, when for each position, the program calls primer3 to design three types of primers: so that the right primer was close to the studied position, the left primer was close to the studied position, and without any of these restrictions.
References 1. FlexPlex27—highly multiplexed rapid DNA identification for law enforcement, kinship, and military applications. Int J Legal Med. Springer; ; : — Segmented continuous-flow multiplex polymerase chain reaction microfluidics for high-throughput and rapid foodborne pathogen detection.
Anal Chim Acta. Elsevier; ; : 51— Detection and localization of surgically resectable cancers with a multi-analyte blood test. NIH Public Access; ; : — Asian Pacific J Cancer Prev. Green MR, Sambrook J.
Cold Spring Harb Protoc; ; Anchored multiplex PCR for targeted next-generation sequencing. Nat Med. Nature Publishing Group; ; 20 : — Mol Diagn Ther. Mol Diagn Ther ; ; 20 : 45— Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. J Vis Exp. NIH Public Access; ; Li H, Durbin R.
Fast and accurate short read alignment with Burrows-Wheeler transform. Primer3—new capabilities and interfaces. Nucleic Acids Res. Oxford University Press; ; 40 : e Comparison of custom capture for targeted next-generation DNA sequencing.
J Mol Diagn. American Society for Investigative Pathology; ; 17 : 64— PLoS One. Public Library of Science; ; 12 : e Sci Transl Med. American Association for the Advancement of Science; ; 10 Comput Biol Chem. Trimmomatic: a flexible trimmer for Illumina sequence data.
Oxford University Press; ; 30 : — Genomic organization of the human PMS2 gene family. Genomics ; ; 30 : — Screening hCHK2 for mutations. If you find any more, please let me know and I can update the list. Best wishes, Steven.
Save my name, email, and website in this browser for the next time I comment. Sign in. Forgot your password? Get help. Privacy Policy. Password recovery. Top Tip Bio. Thank you so much Dr Steven. I need to know if any of these softwares can help me design multiplex pcr primer sets I need something to help me analyse Self Complementary structures Regards. Please enter your comment! Please enter your name here. Load the gene of interest from NCBI, select a search range, sit back and let Primer Premier pick the best possible primers for you.
Primer Premier's search algorithm finds optimal PCR, multiplex and SNP genotyping primers with the most accurate melting temperature using the nearest neighbor thermodynamic algorithm. Primer Premier's search algorithm finds optimal PCR, multiplex and SNP genotyping primers with the most accurate melting temperature using the nearest neighbor thermodynamic algorithm.
Primers are screened for secondary structures, dimers, hairpins, homologies and physical properties before reporting the best ones for your sequence, in ranked order. Equipped with a handy calculator, you can easily manipulate sequences and analyze the results of your primer design. Load the gene of interest from NCBI, select a search range, sit back and let Primer Premier pick the best possible primers for you.
After specifying the SNPs, primers can be designed to amplify them for detection using a probe-based chemistry.
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