Mutagenic primer design for mismatch PCR-RFLP SNP genotyping using a genetic algorithm

IEEE/ACM Transactions on Computational Biology and Bioinformatics
Cheng-Hong YangLi-Yeh Chuang

Abstract

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is useful in small-scale basic research studies of complex genetic diseases that are associated with single nucleotide polymorphism (SNP). Designing a feasible primer pair is an important work before performing PCR-RFLP for SNP genotyping. However, in many cases, restriction enzymes to discriminate the target SNP resulting in the primer design is not applicable. A mutagenic primer is introduced to solve this problem. GA-based Mismatch PCR-RFLP Primers Design (GAMPD) provides a method that uses a genetic algorithm to search for optimal mutagenic primers and available restriction enzymes from REBASE. In order to improve the efficiency of the proposed method, a mutagenic matrix is employed to judge whether a hypothetical mutagenic primer can discriminate the target SNP by digestion with available restriction enzymes. The available restriction enzymes for the target SNP are mined by the updated core of SNP-RFLPing. GAMPD has been used to simulate the SNPs in the human SLC6A4 gene under different parameter settings and compared with SNP Cutter for mismatch PCR-RFLP primer design. The in silico simulation of the proposed GAMPD program showed that it designs...Continue Reading

References

Aug 20, 1992·Nature·P HollandS Krauss
May 11, 1989·Nucleic Acids Research·A HaliassosA Kitzis
Jan 11, 2000·Nucleic Acids Research·S T SherryK Sirotkin
Apr 11, 2001·Bioinformatics·T KämpkeM Mecklenburg
Jun 26, 2003·Nucleic Acids Research·S H ChenC A Hsiung
Jul 23, 2003·Journal of Thrombosis and Haemostasis : JTH·V MooserL Middleton
Feb 19, 2004·British Journal of Cancer·H C Erichsen, S J Chanock
Feb 28, 2004·Bioinformatics·Jain-Shing WuYow-Ling Shiue
Apr 10, 2004·Bioinformatics·Jiren WangWing-Kin Sung
Jun 28, 2005·Nucleic Acids Research·Ruifang ZhangChunyu Liu
Jul 5, 2005·Molecular Interventions·Wolfgang Sadée
Sep 27, 2005·Forensic Science International : Synergy·Anna-Maria Divne, Marie Allen
Jan 3, 2006·Annals of the New York Academy of Sciences·Charles R Cantor
Mar 22, 2006·Oncogene·L J EngleJ E Landers
May 19, 2006·Expert Review of Molecular Diagnostics·Toralf Bernig, Stephen J Chanock
Aug 16, 2006·BMC Bioinformatics·Li-Yeh ChuangHsueh-Wei Chang
Jan 5, 2007·Nucleic Acids Research·Richard J RobertsDana Macelis
Mar 24, 2007·Bioinformatics·Triinu Koressaar, Maido Remm
May 31, 2008·BMC Bioinformatics·Frank M YouOlin D Anderson
Jan 13, 2009·International Journal of Bioinformatics Research and Applications·Jingli WuJian'er Chen
Feb 13, 2009·Computational Biology and Chemistry·Yung-Fu ChenElong Lin
Feb 25, 2009·Bioinformation·Cheng-Hong YangHsueh-Wei Chang
Apr 11, 2009·Autism Research : Official Journal of the International Society for Autism Research·Takeshi SakuraiJoseph D Buxbaum
May 1, 2009·Biotechnology Progress·Cheng-Hong YangHsueh-Wei Chang
Jun 2, 2009·BioTechniques·Hsueh-Wei ChangCheng-Hong Yang
Apr 10, 2010·BMC Bioinformatics·Hsueh-Wei ChangCheng-Hong Yang

❮ Previous
Next ❯

Citations

Jun 25, 2013·Biotechnology Letters·Li-Yeh ChuangCheng-Hong Yang
Apr 11, 2014·BioMed Research International·Yu-Huei ChengCheng-Hong Yang
Jun 1, 2013·IEEE Transactions on Nanobioscience·Li-Yeh ChuangCheng-Hong Yang
Feb 18, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yu-Huei Cheng

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.