Multiobjective optimization-driven primer design mechanism: towards user-specified parameters of PCR primer.

Primers are critical for polymerase chain reaction (PCR) and influence PCR experimental outcomes. Designing numerous combinations of forward and reverse primers involves various primer constraints, posing a computational challenge. Most PCR primer design methods limit parameters because the available algorithms use general fitness functions.

REHUNT: a reliable and open source package for restriction enzyme hunting.

Background: Restriction enzymes are used frequently in biotechnology. However, manual mining of restriction enzymes is challenging. Furthermore, integrating available restriction enzymes into different bioinformatics systems is necessary for many biotechnological applications, such as polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP).

Effective Natural PCR-RFLP Primer Design for SNP Genotyping Using Teaching-Learning-Based Optimization With Elite Strategy.

SNP (single nucleotide polymorphism) genotyping is the determination of genetic variations of SNPs between members of a species. In many laboratories, PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) is a usually used biotechnology for SNP genotyping, especially in small-scale basic research studies of complex genetic diseases. PCR-RFLP requires an available restriction enzyme at least for identify a target SNP and an effective primer pair conforms numerous constraints.

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

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.

PCR-CTPP design for enzyme-free SNP genotyping using memetic algorithm.

In recent years, many single nucleotide polymorphisms (SNPs) have been successfully genotyped by polymerase chain reaction with confronting two-pair primers (PCR-CTPP). However, computation experiments of feasible CTPP primers are still challenging. The melting temperatures between four primers must be within a very narrow range, and many primer constraints need to be conformed to.

Computational intelligence-based polymerase chain reaction primer selection based on a novel teaching-learning-based optimisation.

Specific primers play an important role in polymerase chain reaction (PCR) experiments, and therefore it is essential to find specific primers of outstanding quality. Unfortunately, many PCR constraints must be simultaneously inspected which makes specific primer selection difficult and time-consuming. This paper introduces a novel computational intelligence-based method, Teaching-Learning-Based Optimisation, to select the specific and feasible primers.

Estimation of teaching-learning-based optimization primer design using regression analysis for different melting temperature calculations.

Primers plays important role in polymerase chain reaction (PCR) experiments, thus it is necessary to select characteristic primers. Unfortunately, manual primer design manners are time-consuming and easy to get human negligence because many PCR constraints must be considered simultaneously. Automatic programs for primer design were developed urgently.

Improved candidate drug mining for Alzheimer's disease.

Alzheimer's disease (AD) is the main cause of dementia for older people. Although several antidementia drugs such as donepezil, rivastigmine, galantamine, and memantine have been developed, the effectiveness of AD drug therapy is still far from satisfactory. Recently, the single nucleotide polymorphisms (SNPs) have been chosen as one of the personalized medicine markers.

Specific primer design for the polymerase chain reaction.

The design of primers has a major impact on the success of PCR in relation to the specificity and yield of the amplified product. Here, we introduce the applications of PCR as well as the definition and characteristics for PCR primer design. Recent primer design tools based on Primer3, along with several computational intelligence-based primer design methods which have been applied in primer design, are also reviewed.

Associate PCR-RFLP assay design with SNPs based on genetic algorithm in appropriate parameters estimation.

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is a commonly used laboratory technique and useful in small-scale basic research studies of complex genetic diseases that are associated with single nucleotide polymorphisms (SNPs). Before PCR-RFLP assay for SNP genotyping can be performed, a feasible primer pair observes numerous constraints and an available restriction enzyme for discriminating a target SNP, are required. The computation of feasible PCR-RFLP primers and find available restriction enzymes simultaneously aim at a target SNP is a challenging problem.

Drug-SNPing: an integrated drug-based, protein interaction-based tagSNP-based pharmacogenomics platform for SNP genotyping.

Many drug or single nucleotide polymorphism (SNP)-related resources and tools have been developed, but connecting and integrating them is still a challenge. Here, we describe a user-friendly web-based software package, named Drug-SNPing, which provides a platform for the integration of drug information (DrugBank and PharmGKB), protein-protein interactions (STRING), tagSNP selection (HapMap) and genotyping information (dbSNP, REBASE and SNP500Cancer). DrugBank-based inputs include the following: (i) common name of the drug, (ii) synonym or drug brand name, (iii) gene name (HUGO) and (iv) keywords.

Single nucleotide polymorphism barcoding to evaluate oral cancer risk using odds ratio-based genetic algorithms.

Cancers often involve the synergistic effects of gene-gene interactions, but identifying these interactions remains challenging. Here, we present an odds ratio-based genetic algorithm (OR-GA) that is able to solve the problems associated with the simultaneous analysis of multiple independent single nucleotide polymorphisms (SNPs) that are associated with oral cancer. The SNP interactions between four SNPs-namely rs1799782, rs2040639, rs861539, rs2075685, and belonging to four genes (XRCC1, XRCC2, XRCC3, and XRCC4)-were tested in this study, respectively.

URPD: a specific product primer design tool.

Background: 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 analyzing large sequence but used for a rather straight-forward way of visualizing the primer design process for infrequent users.

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

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 combined bisulfite restriction analysis bioinformatics tool: methyl-typing.

In this chapter, we introduce our developed freeware tool Methyl-Typing. It provides methylation-related bioinformatics with a special focus on combined bisulfite restriction analysis (COBRA). We give an overview of the implementation and program modules for Methyl-Typing.

Confronting two-pair primer design for enzyme-free SNP genotyping based on a genetic algorithm.

Background: 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 polymorphism (SNP) genotyping by electrophoresis without further steps. It is a time- and cost-effective SNP genotyping method that has the advantage of simplicity. However, computation of feasible CTPP primers is still challenging.

SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping.

Background: PCR-restriction fragment length polymorphism (RFLP) assay is a cost-effective method for SNP genotyping and mutation detection, but the manual mining for restriction enzyme sites is challenging and cumbersome. Three years after we constructed SNP-RFLPing, a freely accessible database and analysis tool for restriction enzyme mining of SNPs, significant improvements over the 2006 version have been made and incorporated into the latest version, SNP-RFLPing 2.

Results: The primary aim of SNP-RFLPing 2 is to provide comprehensive PCR-RFLP information with multiple functionality about SNPs, such as SNP retrieval to multiple species, different polymorphism types (bi-allelic, tri-allelic, tetra-allelic or indels), gene-centric searching, HapMap tagSNPs, gene ontology-based searching, miRNAs, and SNP500Cancer.

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 review our own freeware tool V-MitoSNP, giving an overview of its implementation and program workflow. Apart from these, we review several protocols for the graphic input of genes, keywords, gene searching by sequence, mtSNP searching by sequence, restriction enzyme mining, primer design, and virtual electrophoresis for PCR-RFLP genotyping.

Methyl-Typing: an improved and visualized COBRA software for epigenomic studies.

Combined bisulfite restriction analysis (COBRA) is one of the most commonly used methylation quantification methods. However, it focuses on relatively few restriction enzymes. Here, we present Methyl-Typing, a web-based software that provides restriction enzyme mining data for methyl-cytosine-containing sequences following bisulfite-conversion.

Novel generating protective single nucleotide polymorphism barcode for breast cancer using particle swarm optimization.

Background: High-throughput single nucleotide polymorphism (SNP) genotyping generates a huge amount of SNP data in genome-wide association studies. Simultaneous analyses for multiple SNP interactions associated with many diseases and cancers are essential; however, these analyses are still computationally challenging.

Methods: In this study, we propose an odds ratio-based binary particle swarm optimization (OR-BPSO) method to evaluate the risk of breast cancer.

Seq-SNPing: multiple-alignment tool for SNP discovery, SNP ID identification, and RFLP genotyping.

Many sequence-alignment tools were developed to discover single nucleotide polymorphisms (SNPs) derived from resequencing in genomic regions. Whether an identified SNP is indeed a novel SNP or is already contained in dbSNP is often difficult to answer. Here, we describe a freely available software, Seq-SNPing, which is a Java-based software for SNP discovery, and ID identification and editing and visualizating of sequence alignments.

Dynamic programming for single nucleotide polymorphism ID identification in systematic association studies.

Single nucleotide polymorphisms (SNPs) play an important role in personalized medicine. However, the SNP data reported in many association studies provide only the SNP nucleotide/amino acid position, without providing the SNP ID recorded in National Center for Biotechnology Information databases. A tool with the ability to provide SNP ID identification, with a user-friendly interface, is needed.

LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs.

Background: Linkage disequilibrium (LD) mapping 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 services for genotyping.

Results: We developed a freeware called LD2SNPing, which provides a complete package of mining tools for genotyping and LD analysis environments.

Prim-SNPing: a primer designer for cost-effective SNP genotyping.

Many kinds of primer design (PD) software tools have been developed, but most of them lack a single nucleotide polymorphism (SNP) genotyping service. Here, we introduce the web-based freeware "Prim-SNPing," which, in addition to general PD, provides three kinds of primer design functions for cost-effective SNP genotyping: natural PD, mutagenic PD, and confronting two-pair primers (CTPP) PD. The natural PD and mutagenic PD provide primers and restriction enzyme mining for polymerase chain reaction-restriction fragment of length polymorphism (PCR-RFLP), while CTPP PD provides primers for restriction enzyme-free SNP genotyping.

Specific PCR product primer design using memetic algorithm.

To provide feasible primer sets for performing a polymerase chain reaction (PCR) experiment, many primer design methods have been proposed. However, the majority of these methods require a relatively long time to obtain an optimal solution since large quantities of template DNA need to be analyzed. Furthermore, the designed primer sets usually do not provide a specific PCR product size.