DNA sequence is the way of knowing the order of nucleotides within the DNA strands. And DNA Sequence Alignment is to compare two sequences to search for the homology of a newly one of the reference sequence for analyzing the relation between the two DNA sequences. This analysis could lead to know the causative agents of some diseases and the relation between the organisms. This paper is focused on the methods of DNA sequence Alignment and their analysis and related Algorithms.
KEYWORDS
DNA Sequence, DNA alignment, Alignment Algorithms.
Introduction to DNA and its Chemical Composition
Deoxyribose nucleic acid (DNA) is a macro molecule or polymeric chemical compound composed of 4 types of building blocks called deoxyribotids or deoxyribonucleotides.
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Watson and Francis H.C Crick build a model at Cambridge University to explain how the adjacent deoxyribonucleotides are joined in a chain by Phosphodiester bond which links the 5’ Carbon of the deoxyribose sugar of one mononucleotide unit with 3’ carbon of the deoxyribose sugar of other mononucleotide …show more content…
Dot Plot Method
2. Dynamic Programming
3. Heuristic Method
Dot Plot Method: In Dot plot method the characters of two sequences are placed along x-axis and y-axis and a dot is placed when a match occur between the characters. A diagonal line indicate an aligned stretch when the diagonal is complete it means good match otherwise not. The Dot plot method can be used for sequence alignment but it does not give an optimal alignment.
Dynamic Programming:
The Dynamic programming is a method in which sub-problems are solved are solved first, these sub-problems are saved and then all the sub-answers are put together to find the solution of overall problem. The main dynamic programming algorithms for sequence alignment are Needleman-Wunsch algorithm for global alignment and Smith-Waterman algorithm for local alignment.
Needleman-Wunsch algorithm: Saul Needleman and Christian Wunsch developed an algorithm for global alignment called Needleman-Wunsch algorithm. This algorithm finds matches, mismatches and gaps using various scoring matrices. According to this algorithm matches are given higher values while mismatches and gaps are penalized, but gap is more penalized than mismatch. So an optimal alignment is that which has more matches, less mismatches and very less
Deoxyribonucleic acid (DNA) is a molecule found in all forms of life that is passed down from parents to offspring. What makes each DNA unique is the chemical makeup of the molecule sometimes referred to as the “blueprint of life.” (BIO). DNA is made up of nucleotides consisting of a sugar, a phosphate and a base pair. About six million nucleotide base pairs make up DNA in each cell.
Testing phase finds differences in positive/negative documents by the centroid obtained in training phase by ranking each of them. The simple way to estimate similarity between documents and centroid by summing weights of patterns which are in the documents. VII. Experimental Results To determine accurate measures of similarity or difference between documents you depict results by graph pattern and table pattern. The experimental setup consists of relevant documents that you termed as positive and negative documents .i.e
Introduction A mutation is a heritable change that is passed from the mother cell to progeny cells. Mutations may lead to good, bad or neutral phenotypic changes in the organism. They may occur spontaneously as in random DNA replicative errors or may be induced by mutagenic chemicals or radiation. Besides mutations, another way that bacteria achieve gene diversity is through the three known mechanisms for intercellular gene transfer.
Discussion PV92 Gel Electrophoresis Results: Through the usage of gel electrophoresis the correct allele for each sample was able to be determined. Lanes one through three in the gel,were the positive control lanes they contained the PCR cocktail and a known high-quality template for the PCR reaction. First lane contained the sample with the +/+ allele, which had two copies of the ALU repeat allele. The first lane had a band at about 941 base pairs.
1a. Review: Describe three main differences between RNA and DNA. The three main differences between RNA and DNA are as follows: RNA has the sugar ribose instead of deoxyribose, which DNA has, RNA is single-stranded while DNA is double-stranded, and RNA uses uracil instead of thymine. 1b.
DNA Fingerprinting Using Agarose Gel S. Aaron Sowards Bio 122 Lab 04 Brianna Adanitsch Jakob Lester Minhenga Ngijoi 2/21/18 Dr. Chad R. Sethman Abstract DNA fingerprinting is the process of analyzing an individual’s DNA base-pair patterns. The DNA fingerprinting lab involved identifying the suspect using Agarose Gel and Polymerase Chain Reaction. It was found that suspect two s DNA matched the crime scene DNA.
109276 EuDaly 2B CRISPRs Deoxyribonucleic acid (DNA) carries an organism’s genetic material. DNA is inherited from two parents and passed on to offspring. This genetic material makes up the components that construction an organism. The sequence of DNA base pairs determines the traits the offspring will inherit. DNA is responsible for the creation of every protein in the human body.
DNA from the actual parents - Use these chromosomes to make a baby for the DNA profile. Sample D D 248 BP___TPOX #2 Pater. Chromo D 145 BP_D5
Introduction The purpose of this lab is to use control variables to help identify different macromolecules. Biological systems are made up of these four major macromolecules: carbohydrates, lipids, proteins and nucleic acids. Carbohydrates are sugar molecules (monosaccharides, disaccharides, and polysaccharides) which make them the most abundant macromolecule on the earth. Lipids (oils and fats, phospholipids and steroids) are insoluble in water and perform many functions such as energy source, essential nutrients, hormones and insulators (Lehman, 1955).
The sequence of the bases provides the information, so the DNA is like the hard
DNA in Forensic Science DNA is the carrier of genetic information in humans and other living organisms. It has become a very useful tool in forensic science since it was discovered. In forensic science, DNA testing is used to compare the genetic structure of two individuals to establish whether there is a genetic relationship between them. One example of the use of DNA in forensic science that is important in biology today is comparing a suspect’s DNA profile to DNA that was discovered at a crime scene.
The DNA gathered by the group bore positive results only on Test for Deoxyribose; compared to the standard solution, which bore positive results on all chemical tests, namely, Test for Deoxyribose, Test for Phosphate, Test for Purines, and test for Pyrimidines. Introduction Nucleic Acid is one of the essential biochemical molecules
DNA is a complex molecule containing the genetic information that makes up the chromosome. Genomes are the complete instructions for making an organism, consisting of all the genetic material in that organism’s
DNA in forensic science The majority of cells making up the human body are diploid cells carrying identical DNA, with the exception of haploid gametes and red blood cells. Several types of biological evidence such as blood and hair are commonly used in forensic science, which is the scientific study of evidence for crime scene investigations and other legal matters. Forensic science is used for the purpose of DNA analysis, this is the analysis of DNA samples to determine if it came from a particular individual. DNA analysis is done by obtaining DNA samples from an individual; next, a large sample of DNA is produced from amplified selected sequences from the DNA collected.