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Article
Open AccessImproved branch and bound algorithm for detecting SNP-SNP interactions in breast cancer
Single nucleotide polymorphisms (SNPs) in genes derived from distinct pathways are associated with a breast cancer risk. Identifying possible SNP-SNP interactions in genome-wide case–control studies is an impo...
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Article
Open AccessURPD: a specific product primer design tool
Polymerase chain reaction (PCR) plays an important role in molecular biology. Primer design fundamentally determines its results. Here, we present a currently available software that is not located in analyzin...
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Article
Open AccessCpGPAP: CpG island predictor analysis platform
Genomic islands play an important role in medical, methylation and biological studies. To explore the region, we propose a CpG islands prediction analysis platform for genome sequence exploration (CpGPAP).
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Protocol
A Combined Bisulfite Restriction Analysis Bioinformatics Tool: Methyl-Ty**
In this chapter, we introduce our developed freeware tool Methyl-Ty**. It provides methylation-related bioinformatics with a special focus on combined bisulfite restriction analysis (COBRA). We give an overv...
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Article
Open AccessConfronting two-pair primer design for enzyme-free SNP genoty** based on a genetic algorithm
Polymerase chain reaction with confronting two-pair primers (PCR-CTPP) method produces allele-specific DNA bands of different lengths by adding four designed primers and it achieves the single nucleotide polym...
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Article
Open AccessSNP-RFL** 2: an updated and integrated PCR-RFLP tool for SNP genoty**
PCR-restriction fragment length polymorphism (RFLP) assay is a cost-effective method for SNP genoty** and mutation detection, but the manual mining for restriction enzyme sites is challenging and cumbersome....
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Chapter and Conference Paper
Confronting Two-Pair Primer Design Using Particle Swarm Optimization
Polymerase chain reaction with confronting two-pair primers (PCR-CTPP) is a novel PCR technique had been applied to many SNPs (Single Nucleotide Polymorphisms) genoty** experiments successfully in the recent...
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Protocol
An Introduction to Mitochondrial Informatics
In this chapter, we review the public resources available for human mitochondrial DNA and protein related bioinformatics, with a special focus on mitochondrial single nucleotide polymorphisms (mtSNPs). We also...
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Article
Open AccessLD2SN**: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs
Linkage disequilibrium (LD) map** is commonly used to evaluate markers for genome-wide association studies. Most types of LD software focus strictly on LD analysis and visualization, but lack supporting serv...
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Chapter
SNP-Flankplus: SNP ID-Centric Retrieval of Flanking Sequences
PCR is essential for many single nucleotide polymorphism (SNP) genoty** methods. However, the flanking sequences provided by dbSNP of NCBI are usually short and fixed length without further extension, thus m...
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Article
Antibacterial and antioxidant properties of Ramulus Cinnamomi using supercritical CO2 extraction
In this study, crude extracts of Ramulus Cinnamomi from supercritical carbon dioxide under various extraction conditions were examined for their antioxidant and antibacterial activity. The extractions were conduc...
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Chapter
PSO Algorithm for Primer Design
In recent years, polymerase chain reactions (PCR) have been widely applied in medical science. The PCR technique allows a small amount of DNA to be amplified exponentially, thus ensuring that the amount of DNA...
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Chapter
An Integrated Approach Providing Exact SNP IDs from Sequences
Most of the polymorphisms among genomes are single nucleotide polymorphisms (SNPs). An SNP is a variation of the DNA sequence caused by the change of one nucleotide by another, or insertion or deletion of one ...
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Chapter
Microarray Data Feature Selection Using Hybrid GA-IBPSO
DNA microarray examples are generated by a hybridization of mRNA from sample tissues or blood to cDNA (in the case of a spotted array), or hybridization of oligonucleotide of DNA (in the case of Affymetrix chi...
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Chapter and Conference Paper
A Novel GA-Taguchi-Based Feature Selection Method
This work presents a novel GA-Taguchi-based feature selection method. Genetic algorithms are utilized with randomness for “global search” of the entire search space of the intractable search problem. Various g...
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Article
Open AccessV-MitoSNP: visualization of human mitochondrial SNPs
Mitochondrial single nucleotide polymorphisms (mtSNPs) constitute important data when trying to shed some light on human diseases and cancers. Unfortunately, providing relevant mtSNP genoty** information in ...
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Article
Open AccessSNP-RFL**: restriction enzyme mining for SNPs in genomes
The restriction fragment length polymorphism (RFLP) is a common laboratory method for the genoty** of single nucleotide polymorphisms (SNPs). Here, we describe a web-based software, named SNP-RFL**, which ...
