A Novel Teaching-Learning-Based Optimization for Improved Mutagenic Primer Design in Mismatch PCR-RFLP SNP Genotyping

IEEE/ACM Transactions on Computational Biology and Bioinformatics
Yu-Huei Cheng

Abstract

Many single nucleotide polymorphisms (SNPs) for complex genetic diseases are genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in small-scale basic research studies. It is an essential work to design feasible PCR-RFLP primer pair and find out available restriction enzymes to recognize the target SNP for PCR experiments. However, many SNPs are incapable of performing PCR-RFLP makes SNP genotyping become unpractical. A genetic algorithm (GA) had been proposed for designing mutagenic primer and get available restriction enzymes, but it gives an unrefined solution in mutagenic primers. In order to improve the mutagenic primer design, we propose TLBOMPD (TLBO-based Mutagenic Primer Design) a novel computational intelligence-based method that uses the notion of "teaching and learning" to search for more feasible mutagenic primers and provide the latest available restriction enzymes. The original Wallace's formula for the calculation of melting temperature is maintained, and more accurate calculation formulas of GC-based melting temperature and thermodynamic melting temperature are introduced into the proposed method. Mutagenic matrix is also reserved to increase the efficiency of judging a hyp...Continue Reading

References

May 11, 1989·Nucleic Acids Research·A HaliassosA Kitzis
Dec 1, 1993·PCR Methods and Applications·C W DieffenbachG S Dveksler
Aug 26, 1997·Biochemistry·H T Allawi, J SantaLucia
Mar 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·J SantaLucia
Jan 11, 2000·Nucleic Acids Research·S T SherryK Sirotkin
Nov 9, 2002·Bioinformatics·Long-Cheng Li, Rajvir Dahiya
Jul 23, 2003·Journal of Thrombosis and Haemostasis : JTH·V MooserL Middleton
Feb 28, 2004·Bioinformatics·Jain-Shing WuYow-Ling Shiue
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 1, 2006·BMC Genomics·Hsueh-Wei ChangLi-Yeh Chuang
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
Nov 4, 2008·BMC Bioinformatics·Samuel ArvidssonBernd Mueller-Roeber
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
Oct 23, 2009·Nucleic Acids Research·Richard J RobertsDana Macelis
Apr 10, 2010·BMC Bioinformatics·Hsueh-Wei ChangCheng-Hong Yang
Oct 15, 2010·BMC Bioinformatics·Cheng-Hong YangHsueh-Wei Chang
Feb 15, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Cheng-Hong YangLi-Yeh Chuang
Jun 21, 2012·BMC Research Notes·Li-Yeh ChuangCheng-Hong Yang
Jun 26, 2012·Nucleic Acids Research·Andreas UntergasserSteven G Rozen
Jan 15, 2013·Comparative and Functional Genomics·Haitham Sobhy, Philippe Colson
Jun 25, 2013·Biotechnology Letters·Li-Yeh ChuangCheng-Hong Yang
Nov 28, 2013·PloS One·Michael C RileyAmanda Clare

❮ 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.