Introduction to Molecular Biology Information Resources
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Circadian Biology Exercises

Learn more about NCBI bioinformatics resources by following the steps taken by a hypothetical researcher interested in circadian biology.

  Background
Format of Sequence Records
Entrez
BLAST
Structures
Genomes and Maps
Genes
Learn More About Circadian Biology
 

Background back to top

A researcher is interested in writing a grant to study circadian rhythms in mammals. Specifically, she plans to search NCBI resources to find data on a human sleep disorder that has a genetic basis. The researcher is familiar with the data obtained on Drosophila: specific genes including the period gene are known to influence the regular cycling of gene expression that is coordinated with sleep/wake cycles. She hopes to use this knowledge of Drosophila circadian rhythms to help narrow the focus of her research plan. She knows there is a wealth of information available through NCBI. But she is not familiar with the molecular biology databases and resources at NCBI. These exercises guide the researcher through the major NCBI resources.

Format of Sequence Records back to top

 
 
Primary Record
Reference Sequence
Nucleotide
AB002345
NM_022817
Protein
BAA20804
NP_073728
 

Entrez back to top

Find concise summary of genes pertaining to a specific area of research

 
I have received a Request for Proposals on the topic of circadian rhythms. I'd like to study the regulation of a gene important in circadian rhythms, but I haven't decided which gene to follow. I went to Entrez Nucleotide, entered "circadian" and found 668 references--too many! Also, many entries are redundant. How can I get a concise summary of potential genes to follow?
 

    Answer
BLAST back to top

Identify Gene Involved In Sleep Disorder

 

Our research group has obtained the following sequence data from patients with disturbed sleeping patterns:

Nucleotide sequence: gggtgaacag ccgcacggga gtaggtacgc acctgacctc gctggcactg ccgggcaagg cagagggtgt ggcgtcgctc accagccagt gcagctacag cagcaccatc gtccatgtgg gagacaagaa gccgcagccg gagttagaga tggtggaaga tgctgcgagt gggccagaat AA translation: RTGVGTHLTSLALPGKAEGVASLTSQCSYSSTIVHVGDKKP

What gene might this be?

 
    Answer

Normal vs. Disease Gene

 

How does the sequence obtained from patients with sleep disturbances differ from the normal sequence?

Patient sequence: RTGVGTHLTSLALPGKAEGVASLTSQCSYSSTIVHVGDKKP Normal sequence: RTGVGTHLTSLALPGKAESVASLTSQCSYSSTIVHVGDKKP
 
    Answer
Structures back to top

View a structure to examine the significance of a conserved domain

 
I am looking for a 3D structure that contains a conserved domain found in the period 2 protein. What conserved domain should I examine? What structure contains this domain? What can I learn from the structure?
 

    Answer
Genomes and Maps back to top

Find the location of a gene, and download the sequence for the gene plus the promoter region

 
I want to examine how cycles of night and day regulate the expression of the PER2 gene. I need the sequence of the per promoter so that I can create a promoter/reporter construct.
 

    Answer
Genes back to top

Gather sequence data and related information
on a particular genetic locus

 
In my grant proposal, I plan to focus on the human PER2 gene. I'd like a summary of all the sequence data and related information. I'd especially like to find any clinically relevant information that would underscore the importance of studying this particular circadian rhythm gene.
 

    Answer
Learn More About Circadian Biology back to top

  • Related Educational Websites:
    • Howard Hughes Medical Institute Resources on Biological Clocks

    • The Drosophila Molecular Clock Model
    • Abbreviated Version
      Complete Version

    • The Mammalian Molecular Clock Model
    • Complete Version
      Part 4 illustrates how a single base pair substitution in the human Per2 gene results in a shortened sleep cycle in patients with Familial Advanced Sleep Phase Syndrome.
  • References:

  • Revised 12/21/2004