Harvard:Biophysics 101/2007/Notebook:Kaull/2007-3-15
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Homework 3/15/07
See here for assignment.
Part 1: Walk-Through of Analyzing Gene
- Acquire sequence of interest
>example1 CACCCTCGCCAGTTACGAGCTGCCGAGCCGCTTCCTAGGCTCTCTGCGAATACGGACACG CATGCCACCCACAACAACTTTTTAAAAGAATCAGACGTGTGAAGGATTCTATTCGAATTA CTTCTGCTCTCTGCTTTTATCACTTCACTGTGGGTCTGGGCGCGGGCTTTCTGCCAGCTC CGCGGACGCTGCCTTCGTCCAGCCGCAGAGGCCCCGCGGTCAGGGTCCCGCGTGCGGGGT ACCGGGGGCAGAACCAGCGCGTGACCGGGGTCCGCGGTGCCGCAACGCCCCGGGTCTGCG CAGAGGCCCCTGCAGTCCCTGCCCGGCCCAGTCCGAGCTTCCCGGGCGGGCCCCCAGTCC GGCGATTTGCAGGAACTTTCCCCGGCGCTCCCACGCGAAGC
- Send to BLAST - identify gene, and note mutations
>ref|NT_030059.12|Hs10_30314 Homo sapiens chromosome 10 genomic contig, reference assembly Length=44617998 Features flanking this part of subject sequence: 3895 bp at 5' side: hypothetical protein 425 bp at 3' side: HtrA serine peptidase 1 Score = 787 bits (397), Expect = 0.0 Identities = 400/401 (99%), Gaps = 0/401 (0%) Strand=Plus/Plus Query 1 CACCCTCGCCAGTTACGAGCTGCCGAGCCGCTTCCTAGGCTCTCTGCGAATACGGACACG 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 42968870 CACCCTCGCCAGTTACGAGCTGCCGAGCCGCTTCCTAGGCTCTCTGCGAATACGGACACG 42968929 Query 61 CATGCCACCCACAACAACTTTTTAAAAGAATCAGACGTGTGAAGGATTCTATTCGAATTA 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 42968930 CATGCCACCCACAACAACTTTTTAAAAGAATCAGACGTGTGAAGGATTCTATTCGAATTA 42968989 Query 121 CTTCTGCTCTCTGCTTTTATCACTTCACTGTGGGTCTGGGCGCGGGCTTTCTGCCAGCTC 180 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 42968990 CTTCTGCTCTCTGCTTTTATCACTTCACTGTGGGTCTGGGCGCGGGCTTTCTGCCAGCTC 42969049 Query 181 CGCGGACGCTGCCTTCGTCCAGCCGCAGAGGCCCCGCGGTCAGGGTCCCGCGTGCGGGGT 240 |||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||| Sbjct 42969050 CGCGGACGCTGCCTTCGTCCGGCCGCAGAGGCCCCGCGGTCAGGGTCCCGCGTGCGGGGT 42969109 Query 241 ACCGGGGGCAGAACCAGCGCGTGACCGGGGTCCGCGGTGCCGCAACGCCCCGGGTCTGCG 300 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 42969110 ACCGGGGGCAGAACCAGCGCGTGACCGGGGTCCGCGGTGCCGCAACGCCCCGGGTCTGCG 42969169 Query 301 CAGAGGCCCCTGCAGTCCCTGCCCGGCCCAGTCCGAGCTTCCCGGGCGGGCCCCCAGTCC 360 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 42969170 CAGAGGCCCCTGCAGTCCCTGCCCGGCCCAGTCCGAGCTTCCCGGGCGGGCCCCCAGTCC 42969229 Query 361 GGCGATTTGCAGGAACTTTCCCCGGCGCTCCCACGCGAAGC 401 ||||||||||||||||||||||||||||||||||||||||| Sbjct 42969230 GGCGATTTGCAGGAACTTTCCCCGGCGCTCCCACGCGAAGC 42969270
- Get location from genome browser: 124210300 - 124210800 on Chromosome 10
- Identify mutation as an SNP. Search Entrez SNP for the mutant. Obtain a hit:
rs11200638 [Homo sapiens] AGCTCCGCGGACGCTGCCTTCGTCC[A/G]GCCGCAGAGGCCCCGCGGTCAGGGT
- Check OMIM for possible diseases linked to the SNP in question.
In this case, the SNP is linked to a ten-fold increase in wet macular degeneration. The patient can be warned to avoid environmental triggers for the disease (such as excess sunlight and hypertension), and perhaps started on preventative treatments.
Part 2: Contribute a Test Case
>KFG (Kay's Favorite Gene) ATTGCCCCGGTGCTGAGCGGCGCCGCGAGTCGGCCCGAGGCCTCCGGGGACTGCCGTGCCGGGCGGGAGA CCGCCATGGCGACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTCCAGCAGCAGCAGCA GCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGCCG CCACCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCCGCCGCCGCAGGCACAGCCGCTGCTGCCTC AGCCGCAGCCGCCCCCGCCGCCGCCCCCGCCGCCACCCGGCCCGGCTGTGGCTGAGGAGCCGCTGCACCG ACCGTGAGTTTGGGCCCGCTGCAGCTCCCTGTCCCGGCGGGTCCCAGGCTACGGCGGGGATGGCGGTAAC CCTGCAGCCTGCGGGCCGGCGACACGAACCCCCGGCCCCGCAGAGACAGAGTGACCCAGCAACCCAGAGC CCATGAGGGACACCCGCCCCCTCCTGGGGCGAGGCCTTCCCCCACTTCAGCCCCGCTCCCTCACTTGGGT CTTCCCTTGTCCTCTCGCGAGGGGAGGCAGAGCCTTGTTGGGGCCTGTCCTGAATTCACCGAGGGGAGTC ACGGCCTCAGCCCTCTCGCCCTTCGCAGGATGCGAAGAGTTGGGGCGAGAACTTGTTTCTTTTTATTTGC