Harvard:Biophysics 101/2007/Notebook:Kaull/2007-3-15

=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