Campbell Biology (11th Edition)
11th Edition
ISBN: 9780134093413
Author: Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Jane B. Reece
Publisher: PEARSON
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Textbook Question
Chapter 21, Problem 1TYU
Bioinformatics intludes all of the following except
- (A) Using computcr programs foalign DNA sequences.
- (B) using DNA tcchnology to combinr DNA from twodiffcrent soureo in a test tube.
- (C) developing computer-based lools for genome analysis.
- (D) using mathcmatlcal tools to make sense of blological systems.
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Objective: Get a sense of how genomics, the study of the genome in its entirety,needs to think about how to go about its research.
Geonomic DNA is broken up into fragments. The 5’ and 3’ ends of each fragment(a “read”) are sequenced. The sequenced reads are assembled together intocontiguous sequences (“contigs”) based on sequence similarity.
The idea is to sequence enough random fragments so that every nucleotide in thegenome is represented on some read. The number of such fragments needed iscalled the coverage, c.
The coverage c can be calculated by the formula RL/G, where R is the number ofreads sequenced, L is the average length of a read and G is the total length of thegenome. The units of length are bases (b) or base pairs (bp).
Consider a genome whose length is 1000 bp. “Shotgun” sequencing techniquesare applied to the genome, resulting in 20 reads, with an average length of 50 bp.A very important point is that, even though 20 x 50 = 1000, there is no guaranteethat ALL…
Objective: Get a sense of how genomics, the study of the genome in its entirety,needs to think about how to go about its research.
Geonomic DNA is broken up into fragments. The 5’ and 3’ ends of each fragment(a “read”) are sequenced. The sequenced reads are assembled together intocontiguous sequences (“contigs”) based on sequence similarity.
The idea is to sequence enough random fragments so that every nucleotide in thegenome is represented on some read. The number of such fragments needed iscalled the coverage, c.
The coverage c can be calculated by the formula RL/G, where R is the number ofreads sequenced, L is the average length of a read and G is the total length of thegenome. The units of length are bases (b) or base pairs (bp).
Consider a genome whose length is 1000 bp. “Shotgun” sequencing techniquesare applied to the genome, resulting in 20 reads, with an average length of 50 bp.A very important point is that, even though 20 x 50 = 1000, there is no guaranteethat ALL…
Need bioinformatics help.
1) Examine the quality of the raw sequencing data
2) Trim low quality sequences and sequencing adapters from the raw reads
3) Align trimmed reads against the reference genome
4) Count number of reads mapped per annotated gene
5) Differential expression analysis
6) Visualize sequencing reads aligned to the reference genome
7) Gene set enrichment analysis (GSEA)
Choices:
Google Colab
UCSC Genome Browser
fasterq-dump
MultiQC
BLAST
DESeq2
STAR
Gorilla
featureCounts
SNPEff
samtools flagstat
BWA mem
Integrative Genome Viewer (IGV)
LoFreq
Fastp
FastQC
align.seq
2) Trim low quality sequences and sequencing adapters from the raw reads
3) Align trimmed reads against the reference genome
4) Count number of reads mapped per annotated gene
5) Differential expression analysis
6) Visualize sequencing reads aligned to the reference genome
7) Gene set enrichment analysis (GSEA)
Choices:
Google Colab
UCSC Genome Browser…
Chapter 21 Solutions
Campbell Biology (11th Edition)
Ch. 21.1 - Describe the whole-genome shotgun approach.Ch. 21.2 - Prob. 1CCCh. 21.2 - Explain the advantage of the systems biology...Ch. 21.2 - MAKE CONNECTIONS The ENCODE pilot project found...Ch. 21.2 - MAKE CONNECTIONS In Concept 20.2, you learned...Ch. 21.3 - The best estimate is that the human genome...Ch. 21.3 - The Genomes Online Database (GOLD) Website of the...Ch. 21.3 - WHAT IF? What evolutionary processes might...Ch. 21.4 - Discuss the characteristics of mammalian genomes...Ch. 21.4 - VISUAL SKILLS Which of the three mechanisms...
Ch. 21.4 - Contrast the organizations of the rRNA gene family...Ch. 21.4 - MAKE CONNECTIONS Assign each DNA segment at the...Ch. 21.5 - Describe three examples of errors in cellular...Ch. 21.5 - Explain how multiple exons might have arisen in...Ch. 21.5 - What are three ways that transposable elements are...Ch. 21.5 - WHAT IF? In 2005, Icelandic scientists reported...Ch. 21 - How did the Human Genome Project result in more...Ch. 21 - What has been the most significant finding of the...Ch. 21 - Compare genome size, gene number, and gene density...Ch. 21 - Explain how the function of transposable elements...Ch. 21 - How could chromosomal rearrangements lead to the...Ch. 21 - What type of Information can be obtained by...Ch. 21 - Bioinformatics intludes all of the following...Ch. 21 - Homeotic genes (A) encode transcription factors...Ch. 21 - Prob. 3TYUCh. 21 - DRAW IT Below are the amino acid sequences(using...Ch. 21 - EVOLUTION CONNECTION Genes important in the...Ch. 21 - scientific inquiry The scientists mapping the SNPs...Ch. 21 - Prob. 7TYUCh. 21 - SYNTHESIZE YOUR KNOWLEDGE Insects have three...
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- Molecular biologists rely on many, often sophisticated, techniques to pursue their discipline. One may list ultracentrifugation, electron microscopy, X-ray diffraction, electrophoresis, and computer interfacing as fundamental tools. Model organisms provide the raw materials for study. List three "organisms" (or organismic groups) often used by recombinant DNA technologists and describe a major advantage of each group.arrow_forwardWhat is, The ethical implications of gene editing in humans. 1. Introduction: a) Begin with a captivating opening that introduces the topic and its significance. b) Clearly state the thesis statement in this case 2. Body: a) Start with the first main point that discusses the potential benefits of gene editing in humans. b) Transition to the second main point which focuses on the ethical concerns and risks associated with gene editing in humans. Discuss issues like equity fairness and the potential for unintended consequences such as harmful side effects or genetic discrimination. c) Present counterarguments to your points. Acknowledge opposing viewpoints but refute with logical reasoning and supporting evidence emphasizing the importance of considering potential long-term consequences and the need for strict ethical guidelines and regulations. 3. Conclusion: a) Summarize your main points and restate your thesis statement emphasizing the ethical implications of gene editing in…arrow_forwardDNA microarrays... Select an answer and submit. For keyboard navigation, use the up/down arrow keys select an answer. a) can reveal protein-protein interactions. b b) demonstrate differential expression of genes. c) can reveal protein-RNA interactions. d. d) none of the above 2. C.arrow_forward
- Why might hospitals be exempt from the ePrescribing core objective?arrow_forwardBriefly explain about computer-automated high-throughput DNA sequencing ?arrow_forwardExplain how biotechnology and bioinformatics are used to identify microorganisms Explain why biotechnology has replaced many of the traditional diagnostic tools in microbiology Explain why a PCR reaction needs a source of nucleotides in the form of ATP, GTP, CTP and TTP. Explain what primers are and describe their use in PCR reactions Given the results from a PCR/Gel electrophoresis or a DNA sequence; determine the identity of a bacterium or virus...arrow_forward
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