Problem Summary:
Identify Gene Involved In Sleep Disorder |
| Sample User Question |
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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
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What gene might this be?
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| Analysis/Comments |
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These researchers would like to map their sequence data to a specific gene. Using either the nucleotide sequence or the protein sequence as the query and searching the corresponding databases will produce the correct result. Try both approaches and compare which approach produces the most refined results.
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| Flow Chart |
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Nucleotide (blastn):
- Standard nucleotide-nucleotide BLAST [blastn] - Enter patient nucleotide sequence into query box.
- BLAST results - (71 hits total) First hit: 99% identity with (NM_022817.1) Homo sapiens period homolog 2 (Drosophila) (PER2), transcript variant 1, mRNA
Protein (blastp):
- Standard protein-protein BLAST [blastp] - Enter patient protein sequence into query box.
- BLAST results - (19 hits total) First hit: 97% identity with (NP_073728.1) period 2 isoform 2; period, Drosophila, homolog of, 2; period circadian protein 2 [Homo sapiens]
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| Additional Notes |
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Conclusion: The blastp search produced fewer results, while the blastn produced more. The third nucleotide base in a codon can change and still code for the same amino acid; therefore, nucleotide searches tend to be less specific than protein searches.
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