Table of contents

1. Introduction to Genetics51m
2. Mendel's Laws of Inheritance3h 37m
3. Extensions to Mendelian Inheritance2h 41m
4. Genetic Mapping and Linkage2h 28m
5. Genetics of Bacteria and Viruses1h 21m
6. Chromosomal Variation1h 48m
7. DNA and Chromosome Structure56m
8. DNA Replication1h 10m
9. Mitosis and Meiosis1h 34m
10. Transcription1h 0m
11. Translation58m
12. Gene Regulation in Prokaryotes1h 19m
13. Gene Regulation in Eukaryotes44m
14. Genetic Control of Development44m
15. Genomes and Genomics1h 50m
16. Transposable Elements47m
17. Mutation, Repair, and Recombination1h 6m
18. Molecular Genetic Tools19m
- Genetic Cloning
  9m
- Methods for Analyzing DNA
  9m
19. Cancer Genetics29m
- Overview of Cancer
  21m
- Cancer Mutations
  7m
20. Quantitative Genetics1h 26m
21. Population Genetics50m
- Hardy Weinberg
  19m
- Allelic Frequency Changes
  31m
22. Evolutionary Genetics29m

15. Genomes and Genomics

Bioinformatics

Genetics

15. Genomes and Genomics

Bioinformatics

Previous problemNext problem

2:17 minutes

Problem 6a

Textbook Question

You are designing algorithms for the bioinformatic prediction of gene sequences. How might algorithms differ for predicting genes in bacterial versus eukaryotic genomic sequence?

Verified step by step guidance

Understand the structural differences between bacterial and eukaryotic genomes: Bacterial genomes are typically smaller, circular, and lack introns, while eukaryotic genomes are larger, linear, and contain introns and exons.

Consider the presence of operons in bacterial genomes: Bacterial genes are often organized into operons, where multiple genes are transcribed together under a single promoter. Algorithms for bacterial gene prediction should account for this feature.

Account for splicing in eukaryotic genomes: Eukaryotic genes contain introns that are spliced out during mRNA processing. Algorithms for eukaryotic gene prediction must identify exon-intron boundaries using splice site signals (e.g., donor and acceptor sites).

Incorporate promoter and regulatory element differences: Bacterial promoters are simpler and have conserved sequences like the -10 and -35 regions, while eukaryotic promoters are more complex and may include TATA boxes and enhancers. Algorithms should be tailored to detect these specific features.

Use codon bias and GC content: Both bacterial and eukaryotic genomes exhibit codon usage bias and characteristic GC content, which can be used to refine gene predictions. However, the patterns differ between the two, so the algorithm must adapt to the organism type.

Verified video answer for a similar problem:

This video solution was recommended by our tutors as helpful for the problem above

Video duration:

Play a video:

Was this helpful?

Key Concepts

Here are the essential concepts you must grasp in order to answer the question correctly.

Gene Structure Differences

Bacterial genes are typically organized in operons, allowing multiple genes to be transcribed together, while eukaryotic genes are often split by introns and exons, requiring splicing. This structural difference affects how algorithms identify and predict gene sequences, as eukaryotic algorithms must account for splicing and regulatory elements that are less prevalent in bacterial genomes.

Regulatory Elements

Eukaryotic genomes contain complex regulatory elements, such as enhancers and silencers, which influence gene expression. In contrast, bacterial gene regulation is often simpler, relying primarily on promoter regions. Algorithms for eukaryotic gene prediction must incorporate these regulatory sequences to accurately predict gene locations and expression patterns.

Sequence Complexity and Size

Eukaryotic genomes are generally larger and more complex than bacterial genomes, containing more repetitive sequences and non-coding DNA. This complexity poses challenges for algorithms, which must efficiently handle larger datasets and distinguish between functional and non-functional sequences, a task that is less demanding in the more streamlined bacterial genomes.

Watch next

Master Bioinformatics with a bite sized video explanation from Kylia

Start learning

Related Videos

Related Practice

Multiple Choice

Which of the following can be used to identify an open-reading frame?

Go to the National Institute for Child Health and Human Development (http://www.nichd.nih.gov), locate the search box at the top right corner of the homepage, and enter 'RUSP' to search for information on the Recommended Uniform Screening Panel. From the options that appear, select 'Brief History of Newborn Screening' and locate the discussion listing the criteria for adding a disease to the RUSP list. What are the criteria for listing a disease on the RUSP list?

346

views

Textbook Question

What are community-based genetic screening programs? What is the intent of such screening programs? Why are members of specific communities or populations offered the chance to participate in such programs?

478

views

Textbook Question

What is bioinformatics, and why is this discipline essential for studying genomes? Provide two examples of bioinformatics applications.

539

views

Textbook Question

Do you think it is important that participation in community-based genetic screening be entirely voluntary? Why or why not?

425

views

Textbook Question

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.

946

views

Textbook Question

Go to http://blast.ncbi.nlm.nih.gov/Blast.cgi and follow the links to nucleotide BLAST. Type in the sequence below; it is broken up into codons to make it easier to copy.

5' ATG TTC GTC AAT CAG CAC CTT TGT GGT TCT CAC CTC GTT GAA GCTTTG TAC CTT GTT TGC GGT GAA CGT GGT TTC TTC TAC ACT CCT AAG ACT TAA 3'

As you will note on the BLAST page, there are several options for tailoring your query to obtain the most relevant information. Some are related to which sequences to search in the database. For example, the search can be limited taxonomically (e.g., restricted to mammals) or by the type of sequences in the database (e.g., cDNA or genomic). For our search, we will use the broadest database, the 'Nucleotide collection (nr/nt).' This is the nonredundant (nr) database of all nucleotide data (nt) in GenBank and can be selected in the 'Database' dialogue box. Other parameters can also be adjusted to make the search more or less sensitive to mismatches or gaps. For our purposes, we will use the default setting, which is automatically presented. Press 'BLAST' to search. What can you say about the DNA sequence?

340

views

Textbook Question

In the course of the Drosophila melanogaster genome project, the following genomic DNA sequences were obtained. Try to assemble the sequences into a single contig.

5' TTCCAGAACCGGCGAATGAAGCTGAAGAAG 3'

5' GAGCGGCAGATCAAGATCTGGTTCCAGAAC 3'

5' TGATCTGCCGCTCCGTCAGGCATAGCGCGT 3'

5' GGAGAATCGAGATGGCGCACGCGCTATGCC 3'

5' CCATCTCGATTCTCCGTCTGCGGGTCAGAT 3'

Go to the URL provided in Problem 14, and using the sequence you have just assembled, perform a blastn search in the 'Nucleotide collection (nr/nt)' database. Does the search produce sequences similar to your assembled sequence, and if so, what are they? Can you tell if your sequence is transcribed, and if it represents protein-coding sequence? Perform a tblastx search, first choosing the 'Nucleotide collection (nr/nt)' database and then limiting the search to human sequences by typing Homo sapiens in the organism box. Are homologous sequences found in the human genome? Annotate the assembled sequence.

422

views

Show more practices

Download the Mobile app

Privacy

Do not sell my personal information

Accessibility

Patent notice

Sitemap