Textbook Question
What is bioinformatics, and why is this discipline essential for studying genomes? Provide two examples of bioinformatics applications.
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Ch. 18 - Genomics, Bioinformatics, and Proteomics
Klug10th EditionEssentials of GeneticsISBN: 9780135588789
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Table of contents
- Ch. 1 - Introduction to Genetics16
- Ch. 2 - Mitosis and Meiosis28
- Ch. 3 - Mendelian Genetics37
- Ch. 4 - Modification of Mendelian Ratios53
- Ch. 5 - Sex Determination and Sex Chromosomes32
- Ch. 6 - Chromosome Mutations: Variation in Number and Arrangement37
- Ch. 7 - Linkage and Chromosome Mapping in Eukaryotes36
- Ch. 8 - Genetic Analysis and Mapping in Bacteria and Bacteriophages24
- Ch. 9 - DNA Structure and Analysis38
- Ch. 10 - DNA Replication29
- Ch. 11 - Chromosome Structure and DNA Sequence Organization22
- Ch. 12 - The Genetic Code and Transcription36
- Ch. 13 - Translation and Proteins27
- Ch. 14 - Gene Mutation, DNA Repair, and Transposition34
- Ch. 15 - Regulation of Gene Expression in Bacteria22
- Ch. 16 - Regulation of Gene Expression in Eukaryotes37
- Ch. 17 - Recombinant DNA Technology27
- Ch. 18 - Genomics, Bioinformatics, and Proteomics30
- Ch. 19 - The Genetics of Cancer21
- Ch. 20 - Quantitative Genetics and Multifactorial Traits37
- Ch. 21 - Population and Evolutionary Genetics45
Chapter 18, Problem 8
BLAST searches and related applications are essential for analyzing gene and protein sequences. Define BLAST, describe basic features of this bioinformatics tool, and give an example of information provided by a BLAST search.
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Step 1: Define BLAST by explaining that it stands for Basic Local Alignment Search Tool, which is a bioinformatics algorithm used to compare an input nucleotide or protein sequence against a database of sequences to find regions of similarity.
Step 2: Describe the basic features of BLAST, including its ability to quickly identify local alignments rather than global alignments, its use of scoring matrices to evaluate sequence similarity, and its statistical framework to assess the significance of matches.
Step 3: Explain that BLAST can be used for different types of searches such as nucleotide-to-nucleotide (blastn), protein-to-protein (blastp), and translated searches (blastx), depending on the input and database sequences.
Step 4: Discuss how BLAST outputs include important information such as the alignment score, E-value (expectation value) which indicates the likelihood of the match occurring by chance, and the identity percentage showing how similar the sequences are.
Step 5: Provide an example of information from a BLAST search, such as identifying a gene in an unknown DNA sequence by finding a highly similar known gene in the database, or predicting the function of a protein by comparing it to proteins with known functions.
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Key Concepts
Here are the essential concepts you must grasp in order to answer the question correctly.
BLAST (Basic Local Alignment Search Tool)
BLAST is a bioinformatics algorithm used to compare an input nucleotide or protein sequence against a database to find regions of local similarity. It helps identify homologous sequences, infer functional and evolutionary relationships, and locate conserved domains.
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Features of BLAST
BLAST performs rapid sequence alignments by breaking sequences into smaller words and extending matches to find high-scoring segment pairs. It provides statistical significance scores (E-values), alignment scores, and identifies similar sequences with varying degrees of identity and coverage.
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Information Provided by a BLAST Search
A BLAST search outputs aligned sequences with similarity scores, E-values indicating match significance, and annotations such as gene or protein names. For example, it can reveal potential functions of an unknown gene by matching it to known genes in the database.
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Related Practice
Textbook Question
Annotation involves identifying genes and gene-regulatory sequences in a genome. List and describe characteristics of a genome that are hallmarks for identifying genes in an unknown sequence. What characteristics would you look for in a bacterial genome? A eukaryotic genome?
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Textbook Question
How do high-throughput techniques such as computer-automated, next-generation sequencing, and mass spectrometry facilitate research in genomics and proteomics? Explain.
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Textbook Question
Describe three major goals of the Human Genome Project.
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Textbook Question
Describe the human genome in terms of genome size, the percentage of the genome that codes for proteins, how much is composed of repetitive sequences, and how many genes it contains. Describe two other features of the human genome.
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Textbook Question
Recall that when the HGP was completed, more than 40 percent of the genes identified had unknown functions. The PANTHER database provides access to comprehensive and current functional assignments for human genes (and genes from other species).
Go to http://www.pantherdb.org/data/. In the frame on the left side of the screen locate the 'Quick links' and use the 'Whole genome function views' link to a view of a pie chart of current functional classes for human genes. Mouse over the pie chart to answer these questions. What percentage of human genes encode transcription factors? Cytoskeletal proteins? Transmembrane receptor regulatory/adaptor proteins?
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