if you want to remove an article from website contact us from top.

    true or false. sequence read 2 is identical to the reference genome.

    James

    Guys, does anyone know the answer?

    get true or false. sequence read 2 is identical to the reference genome. from EN Bilgi.

    Understanding a Genome Sequence

    When you have read Chapter 7, you should be able to:

    An official website of the United States government

    Log in Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation Bookshelf

    Browse Titles Advanced

    Help

    Genomes. 2nd edition.

    Show details

    ContentsCurrent edition published by Garland Science

    < PrevNext >

    Chapter 7Understanding a Genome Sequence

    Go to:

    Learning outcomes

    When you have read Chapter 7, you should be able to:

    Describe the strengths and weaknesses of the computational and experimental methods used to analyze genome sequences

    Describe the basis of open reading frame (ORF) scanning, and explain why this approach is not always successful in locating genes in eukaryotic genomes

    Outline the various experimental methods used to identify parts of a genome sequence that specify RNA molecules

    Define the term ‘homology’ and explain why homology is important in computer-based studies of gene function

    Evaluate the limitations of homology analysis, using the yeast genome project as an example

    Describe the methods used to inactivate individual genes in yeast and mammals, and explain how inactivation can lead to identification of the function of a gene

    Give outline descriptions of techniques that can be used to obtain more detailed information on the activity of a protein coded by an unknown gene

    Describe how the transcriptome and proteome are studied

    Explain how protein interaction maps are constructed and indicate the key features of the yeast map

    Evaluate the potential and achievements of comparative genomics as a means of understanding a genome sequence

    a genome sequence is not an end in itself. A major challenge still has to be met in understanding what the genome contains and how the genome functions. The former is addressed by a combination of computer analysis and experimentation, with the primary aim of locating the genes and their control regions. The first part of this chapter is devoted to these methods. The second question - understanding how the genome functions - is, to a certain extent, merely a different way of stating the objectives of molecular biology over the last 30 years. The difference is that in the past attention has been directed at the expression pathways for individual genes, with groups of genes being considered only when the expression of one gene is linked to that of another. Now the question has become more general and relates to the expression of the genome as a whole. The techniques used to address this topic will be covered in the latter parts of this chapter.

    Go to:

    7.1. Locating the Genes in a Genome Sequence

    Once a DNA sequence has been obtained, whether it is the sequence of a single cloned fragment or of an entire chromosome, then various methods can be employed to locate the genes that are present. These methods can be divided into those that involve simply inspecting the sequence, by eye or more frequently by computer, to look for the special sequence features associated with genes, and those methods that locate genes by experimental analysis of the DNA sequence. The computer methods form part of the methodology called bioinformatics, and it is with these that we begin.

    7.1.1. Gene location by sequence inspection

    Sequence inspection can be used to locate genes because genes are not random series of nucleotides but instead have distinctive features. These features determine whether a sequence is a gene or not, and so by definition are not possessed by non-coding DNA. At present we do not fully understand the nature of these specific features, and sequence inspection is not a foolproof way of locating genes, but it is still a powerful tool and is usually the first method that is applied to analysis of a new genome sequence.

    The coding regions of genes are open reading frames

    Genes that code for proteins comprise open reading frames (ORFs) consisting of a series of codons that specify the amino acid sequence of the protein that the gene codes for (see Figure 1.17). The ORF begins with an initiation codon - usually (but not always) ATG - and ends with a termination codon: TAA, TAG or TGA (Section 3.3.2). Searching a DNA sequence for ORFs that begin with an ATG and end with a termination triplet is therefore one way of looking for genes. The analysis is complicated by the fact that each DNA sequence has six reading frames, three in one direction and three in the reverse direction on the complementary strand (Figure 7.1), but computers are quite capable of scanning all six reading frames for ORFs. How effective is this as a means of gene location?

    Figure 7.1

    A double-stranded DNA molecule has six reading frames. Both strands are read in the 5′→3′ direction. Each strand has three reading frames, depending on which nucleotide is chosen as the starting position.

    The key to the success of ORF scanning is the frequency with which termination codons appear in the DNA sequence. If the DNA has a random sequence and a GC content of 50% then each of the three termination codons - TAA, TAG and TGA - will appear, on average, once every 43 = 64 bp. If the GC content is > 50% then the termination codons, being AT-rich, will occur less frequently but one will still be expected every 100–200 bp. This means that random DNA should not show many ORFs longer than 50 codons in length, especially if the presence of a starting ATG is used as part of the definition of an ‘ORF’. Most genes, on the other hand, are longer than 50 codons: the average lengths are 317 codons for , 483 codons for , and approximately 450 codons for humans. ORF scanning, in its simplest form, therefore takes a figure of, say, 100 codons as the shortest length of a putative gene and records positive hits for all ORFs longer than this.

    Source : www.ncbi.nlm.nih.gov

    Initial sequencing and analysis of the human genome

    The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

    Published: 15 February 2001

    Initial sequencing and analysis of the human genome

    International Human Genome Sequencing Consortium

    volume 409, pages

    860–921 (2001)Cite this article

    266k Accesses 15459 Citations 1247 Altmetric Metrics details

    A Corrigendum to this article was published on 01 August 2001

    An Erratum to this article was published on 01 June 2001

    Abstract

    The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

    Download PDF

    Main

    The rediscovery of Mendel's laws of heredity in the opening weeks of the 20th century1,2,3 sparked a scientific quest to understand the nature and content of genetic information that has propelled biology for the last hundred years. The scientific progress made falls naturally into four main phases, corresponding roughly to the four quarters of the century. The first established the cellular basis of heredity: the chromosomes. The second defined the molecular basis of heredity: the DNA double helix. The third unlocked the informational basis of heredity, with the discovery of the biological mechanism by which cells read the information contained in genes and with the invention of the recombinant DNA technologies of cloning and sequencing by which scientists can do the same.

    The last quarter of a century has been marked by a relentless drive to decipher first genes and then entire genomes, spawning the field of genomics. The fruits of this work already include the genome sequences of 599 viruses and viroids, 205 naturally occurring plasmids, 185 organelles, 31 eubacteria, seven archaea, one fungus, two animals and one plant.

    Here we report the results of a collaboration involving 20 groups from the United States, the United Kingdom, Japan, France, Germany and China to produce a draft sequence of the human genome. The draft genome sequence was generated from a physical map covering more than 96% of the euchromatic part of the human genome and, together with additional sequence in public databases, it covers about 94% of the human genome. The sequence was produced over a relatively short period, with coverage rising from about 10% to more than 90% over roughly fifteen months. The sequence data have been made available without restriction and updated daily throughout the project. The task ahead is to produce a finished sequence, by closing all gaps and resolving all ambiguities. Already about one billion bases are in final form and the task of bringing the vast majority of the sequence to this standard is now straightforward and should proceed rapidly.

    The sequence of the human genome is of interest in several respects. It is the largest genome to be extensively sequenced so far, being 25 times as large as any previously sequenced genome and eight times as large as the sum of all such genomes. It is the first vertebrate genome to be extensively sequenced. And, uniquely, it is the genome of our own species.

    Much work remains to be done to produce a complete finished sequence, but the vast trove of information that has become available through this collaborative effort allows a global perspective on the human genome. Although the details will change as the sequence is finished, many points are already clear.

    • The genomic landscape shows marked variation in the distribution of a number of features, including genes, transposable elements, GC content, CpG islands and recombination rate. This gives us important clues about function. For example, the developmentally important HOX gene clusters are the most repeat-poor regions of the human genome, probably reflecting the very complex coordinate regulation of the genes in the clusters.

    • There appear to be about 30,000–40,000 protein-coding genes in the human genome—only about twice as many as in worm or fly. However, the genes are more complex, with more alternative splicing generating a larger number of protein products.

    • The full set of proteins (the ‘proteome’) encoded by the human genome is more complex than those of invertebrates. This is due in part to the presence of vertebrate-specific protein domains and motifs (an estimated 7% of the total), but more to the fact that vertebrates appear to have arranged pre-existing components into a richer collection of domain architectures.

    • Hundreds of human genes appear likely to have resulted from horizontal transfer from bacteria at some point in the vertebrate lineage. Dozens of genes appear to have been derived from transposable elements.

    • Although about half of the human genome derives from transposable elements, there has been a marked decline in the overall activity of such elements in the hominid lineage. DNA transposons appear to have become completely inactive and long-terminal repeat (LTR) retroposons may also have done so.

    • The pericentromeric and subtelomeric regions of chromosomes are filled with large recent segmental duplications of sequence from elsewhere in the genome. Segmental duplication is much more frequent in humans than in yeast, fly or worm.

    • Analysis of the organization of Alu elements explains the longstanding mystery of their surprising genomic distribution, and suggests that there may be strong selection in favour of preferential retention of Alu elements in GC-rich regions and that these ‘selfish’ elements may benefit their human hosts.

    Source : www.nature.com

    Week 5 Monday PRQs Flashcards

    Start studying Week 5 Monday PRQs. Learn vocabulary, terms, and more with flashcards, games, and other study tools.

    Week 5 Monday PRQs

    Modern methods of massively parallel sequencing include devices for detecting fluorescence or visible light as each:

    Click card to see definition 👆

    nucleotide is incorporated during synthesis.

    Each nucleotide is marked with fluorescent dye, and a trace of fluorescent intensities helps identify sequences.

    Click again to see term 👆

    What is the difference between PCR and Sanger sequencing with regard to the materials needed to perform these reactions?

    Click card to see definition 👆

    Dideoxynucleotides are needed in Sanger sequencing but not in PCR.

    Both processes involve DNA replication, which requires DNA, DNA polymerase, and primers. Only Sanger sequencing requires dideoxynucleotides.

    Click again to see term 👆

    1/46 Created by benk122

    Terms in this set (46)

    Modern methods of massively parallel sequencing include devices for detecting fluorescence or visible light as each:

    nucleotide is incorporated during synthesis.

    Each nucleotide is marked with fluorescent dye, and a trace of fluorescent intensities helps identify sequences.

    What is the difference between PCR and Sanger sequencing with regard to the materials needed to perform these reactions?

    Dideoxynucleotides are needed in Sanger sequencing but not in PCR.

    Both processes involve DNA replication, which requires DNA, DNA polymerase, and primers. Only Sanger sequencing requires dideoxynucleotides.

    Which factors make sequencing by the Sanger chain-termination method possible? Select all that apply.

    - Complementary single-stranded nucleic acid sequences can come together to form a duplex molecule.

    - New nucleotides are added only to the 3' end of a growing DNA strand.

    - Duplex nucleic acid molecules can be separated by size by means of gel electrophoresis.

    - A DNA strand whose 3' end terminates in a dideoxynucleotide cannot be elongated.

    Restriction enzymes are an essential component of PCR.

    False

    The DNA sequence shown below comes from part of the TP53 gene. It encodes the last amino acids of the p53 protein, which is normally 393 amino acids long. The underlined codon indicates the correct reading frame of this gene. The lower strand of the gene is used as the template during the transcription of mRNA from this gene. The first T on the 5' end is at position 1.

    ...TTCAAGACAGAAGGGCCTGACTCAGACTGACATTCTCC-3'

    ...AAGTTCTGTCTTCCCGGACTGAGTCTGACTGTAAGAGG-5'

    T/F: A mutation that changes the nucleotide at position 23 from C to G is a nonsense mutation.

    True

    The change from C to G converts Ser to a stop codon, leading to a nonsense mutation.

    Which pair of people has the exact same genome?

    monozygotic twins

    The DNA sequence shown below comes from part of the TP53 gene. It encodes the last amino acids of the p53 protein, which is normally 393 amino acids long. The underlined codon indicates the correct reading frame of this gene. The lower strand of the gene is used as the template during the transcription of mRNA from this gene. The first T on the 5' end is at position 1.

    ...TTCAAGACAGAAGGGCCTGACTCAGACTGACATTCTCC-3'

    ...AAGTTCTGTCTTCCCGGACTGAGTCTGACTGTAAGAGG-5'

    T/ F A mutation that changes the nucleotide at position 20 from A to G is a silent mutation.

    False

    A change from A to G changes the amino acid from Asp to Gly. This is a missense mutation.

    In DNA sequencing, the newly synthesized DNA strand that is complementary and anti-parallel to a template DNA strand is called a sequence read.

    True

    The sequencing read is formed in the opposite direction of the template strand following the primer.

    Sequencing reads can be aligned to a reference genome (i.e., human genome) to identify single nucleotide variants and potential disease-related mutations.

    True

    Which group lists the levels of genetic information in order from smallest to largest.

    exon, gene; chromosome; genome

    Sign up and see the remaining cards. It’s free!

    Boost your grades with unlimited access to millions of flashcards, games and more.

    Continue with Google

    Continue with Facebook

    Already have an account?

    Recommended textbook explanations

    Biology 1st Edition

    Kenneth R. Miller, Levine

    2,591 explanations Biology 1st Edition

    Kenneth R. Miller, Levine

    2,470 explanations

    Texas Science Fusion: Grade 7

    1st Edition Holt McDougal 562 explanations Biology 1st Edition Stephen Nowicki 1,895 explanations

    Sets found in the same folder

    Week 4 Wednesday PRQs

    20 terms benk122

    Biology Ch35 Launchpad q's

    59 terms SabrinaNguyen2

    Biology: How Life Works | Ch 42 Learning Curve

    13 terms studyanon3435PLUS

    Chapter 41

    16 terms PeytonY22

    Other sets by this creator

    Week 6 Wednesday PRQs

    10 terms benk122

    Week 6 Monday PRQs

    12 terms benk122

    Week 5 Wednesday PRQs

    22 terms benk122

    Week 4 Friday PRQs

    23 terms benk122

    Source : quizlet.com

    Do you want to see answer or more ?
    James 12 day ago
    4

    Guys, does anyone know the answer?

    Click For Answer