For most sequences at position 4 and 5 we observe only the nucleotides G and T, respectively. There may be rare cases where other nucleotides may also be found. To consider such observations, we need to do a process called additive smoothing or Laplace smoothing to smooth the categorical data. [9] In this case, we add 4 sequences: AAAAAAAAA, CCCCCCCCC, GGGGGGGG, TTTTTTTTT. These sequences would give us a pseudocount of 1 at each position called the Laplace pseudocount. fA,1 = (3+1)/(10+4) fC,1 = (3+1)/(10+4) fG,1 = (3+1)/(10+4) fT,1 = (3+1)/(10+4) Updating the matrix given in Figure 4, we obtain the new position weight matrix calculated. It is given as a table below. Table 1: Corresponding PWM for given sequences with Laplace pseudocounts Nucleotide …show more content…
Nucleotide 1 2 3 4 5 6 7 8 9 A 0.286 0.357 0.143 0.071 0.071 0.500 0.643 0.071 0.143 C 0.357 0.143 0.214 0.071 0.071 0.071 0.071 0.143 0.143 G 0.143 0.214 0.500 0.786 0.071 0.143 0.214 0.714 0.214 T 0.214 0.286 0.143 0.071 0.786 0.071 0.071 0.071 0.500 3.3 Log-odds
A P A T C G i 0 1 2 3 2. In the next step we move forward by comparing successive characters of pattern P to "parallel" characters of genome String S, moving from one character to the next if they match. 3.
Some of these errors include the excessive addition of the mutant undigested DNA to the MU tube in which the entire sample of the DNA (approximately 4 µL) was added instead of 2.5 µL. The next experimental error was the underloading of the DNA samples into the wells. When the DNA was put into the well, all of the DNA were underloaded and after the gel undergone electrophoresis, bands were not present. As seen in Figure 2a in the results section, only bands for the marker were shown and the rest were not shown. Comparing this to the expected results reveals that there was an error in this phase of the experiment. Due to the fact that we have no bands present and are thus unable to compare them the expected results, a number of other factors could have gone wrong as well.
The dna sequence that contains a lot of base
Principles of Human Physiology, 4e (Stanfield) Chapter 2 The Cell: Structure and Function 2.1 Multiple Choice Questions Figure 2.1 Using Figure 2.1, answer the following questions: 1) Which of the following nucleotide sequences accurately reflects the mRNA that would be produced from the double-stranded DNA pictured in Figure 2.1? A) TGTCTCACTGTCTTG B)
Many people are familiar with the spiral staircase appearance of DNA. The twisted pieces on the outside of the ladder are called the sugar phosphate backbone. The rungs of the latter consist of nitrogenous bases called Adenine, Thymine, Guanine, and cytosine with Adenine always pairing with thymine and guanine always pairing with cytosine. A phosphate group, a sugar, and one of the four nitrogenous bases bond to create a nucleotide which makes up DNA. In fact, DNA stands for Deoxyribonucleic acid with nucleic representing the nucleotides in DNA.
The DNA fragment was excise from the agarose gel with a clean, sharp scalped. The gel slice was weighed in a colorless tube and 3 volumes of Buffer QG was added to 1 volume of gel. The gel was incubated at 50°C until the gel slice has completely dissolve and to help dissolve better, the gel was mix by vortexing the tube every 2-3 min during incubation. After the gel have dissolved, 1 gel volume of isopropanol was added to the sample and it was mixed. The QIAquick spin column was placed in a provided 2 ml collection tube and to bind DNA, the sample was applied to the QIAquick column, and centrifuge for 1 min.
Single Stranded C.) Circular From the choices I am given, I can safely eliminate choice c. I am then left with choice A and choice B. From studying the material, it is easy to recognize that choice B is the wrong answer because DNA is never single stranded and always likes to pair up. Which leaves the correct answer choice A. Through the process of elimination and recognition, I was able to get to the correct answer.
The gel consists of a penetrable matrix through which molecules can travel when triggered by an electric current. Smaller molecules migrate through the gel more quickly and consequently travel further. Larger fragments that migrate slowly travel a shorter distance. The result is that the specific molecules are separated by size in electrophoresis. A short tandem repeat (STR) in DNA is a quantity of polymorphisms that occurs when a pattern of two or more nucleotides is repeated and the recurrent sequences are directly adjacent to each other.
(DNA: Structure, n.d.) The bases pair with each other on either side of the “ladder”; adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine(C). The order of these bases determines the genetic code of the DNA, and even though 99% of these genes are arranged in the same order the small difference is a big part of what makes you, you! (What are DNA and Genes?,
The closer the plot to a slope of 0, the less impact from direct mutation pressure. When the slope is 1, the codon usage bias is fully formed by direct mutation pressure and neutrality. GC1 and GC2 contents were calculated using Perl
First one has to know the Chargaff base pairing rule. According to this rule; in DNA, Adenosine (A) pairs with thymidine (T) in double bonds while cytidine pairs with the guanosine in triple bonds. In RNA, thymidine is replaced with the uridine(U). The picture below shows how these bonds occur in DNA
1.0 INTRODUCTION Deoxyribonucleic acid (DNA) is the biomolecule that carries genetic information. Eukaryotic DNA is localized in the nucleus of cells on linear chromosomes. Genes are transcribed from DNA into ribonucleic acid (RNA), which is transported out of the nucleus to be translated into proteins that carry out most of the biological functions inside and outside of cells. The bases of DNA make up codons for specific amino acids, the building blocks of proteins. The knowledge that DNA may contain the blueprint for all biological processes led to a lot of interest in its structure.
The assignment for this analysis is DNA structure and base pairing of DNA. The directions for the assignment are as follows: In part, A students are to label the key components of a strand of DNA. Part B directions are to write the compliment (partner) of each nitrogenous base to construct the complementary DNA strand. These directions are very clear and precise.
Moreover, the study utilizes advanced techniques such as X-ray crystallography to answer questions regarding chromatin structure which makes it an invaluable learning experience that is not available at my home
After incubation, 200 µl of 100% ethanol was added to the lysate. The sample was then washed and centrifuged following the manufacturer’s recommendations. Nucleic acid was eluted with 100 µl of elution buffer provided in the kit. Oligonucleotide Primer. Primers used were supplied from Metabion (Germany) are listed in table (1).