Genetic Tools from Gene Link vs Genetic Algorithms

This application from Gene Link, Inc.for iPhone/iPod/iPad is geared towards life scientists, including college and graduate students for laboratory bench calculations and a quick short course in molecular genetics. Topics included are all related to nucleic acids research with an emphasis on utilizing properties that increase specific predetermined properties e.g duplex stability. The app also has advanced modules for setup of Polymerase Chain Reaction (PCR) and Quantitative Real Time PCR (Q-PCR). The main focus of this app is to have a handy source of calculation modules and quick reference sections for designing and executing experiments involving PCR and Q-PCR. These techniques are routinely used in a molecular genetics laboratory for all type of research involving DNA. These vary from simple DNA amplification and confirmation to complex allele and genotyping for diagnostics. The application has sections to encourage users to design primer and probes using modified bases as substitutes for the natural four bases to enable specificity and increase nuclease resistance. The application is divided into two sections; the Tools sections are an assortment of convenient calculators for the life scientist and the Reference section is for basic genetic information. A. Tools 1. Oligo Tm: A robust oligo melting temperature calculation module using three methods; it also calculates other physical attributes. 2. Oligo Resuspension 5. Oligo Dilution 6. PCR & QPCR: Convenient calculator for multiple reaction setup for PCR, TaqMan QPCR and Molecular Beacon QPCR setup. Includes stock solution information and cycling profiles 7. Molarity Calculator 8. Reagent Dilution 9. Measurement Convertor: A convenient selection of calculators to convert length, area, mass, temperature and volume units. 10. Genetic Code Translator: Enter DNA sequence to see coding pattern. B. Reference A selection of topics, relevant to life scientists for quick access to basic information. This section includes the following sections and sub sections. 1. Nucleic Acid Basics -Bases -Base Pairing -Oligo Types -Modification Sites 2. Modifications Table: A list of common modifications with molecular structure and basic properties. 3. Dye & Quencher Table: A convenient list of fluorophores and quencher matching the emission max. 4. Duplex Stability & Nuclease Resistance -Modifications Table. -Applications & Recommended Modifications: • Antisense Gene Target • siRNA-RNA Interference • PCR Primers • QPCR Probes • SNP Genotyping & Allelic Discrimination • Fluorescent in situ Hybridization Probes (FISH) . 5. Gene Information: Simply enter the accession number and retrieve detailed gene information from NCBI database, 6. Amino Acid Table: Molecular structure and detailed physical properties of all amino acids. 7. Translation Table: Genetic code for all amino acids. 8. Codon Picker: Select codon sequence and see the corresponding amino acid and detailed information.

Genetic algorithms are one of the search and optimisation methods. The aim of optimisation is to increase efficiency in reaching a certain optimal value. Genetic algorithms are based on the mechanisms of natural selection and heredity. The basic genetic algorithm is built from three operations: reproduction, crossing, and mutation. Genetic algorithms operate on populations of coding sequences and use random selection rules to search for the global optimal value. However, these random rules are defined to give the appropriate direction of the search (through various selection mechanisms or scaling of fitness functions). This basic procedure is enhanced by certain genetic manipulations, such as those seen in nature. They include the mechanisms of dominance, diploidy, inversion, and other reconfiguration mechanisms that occur at the chromosome level. Users can design textual or graphical scaling patterns for the fitness function and then use them in simulations. The application also provides a preliminary analysis of statistical data concerning the distribution of the fitness function in the population. The program allows the user to compare non-random procedures (e.g. scaling of fitness functions) by using the same pseudorandom sequence (for procedures requiring randomization, such as selection, etc.) in successive simulations. In order to better visualize the genetic processes taking place during the simulation, some of them are presented to the user using animations. Additionally, some of the data obtained from simulations can be saved and shared.