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.

Format of Sequence Records
Genomes and Maps
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

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?

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?


Normal vs. Disease Gene


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

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?

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.

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.

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