Harvard:Biophysics 101/2007/Notebook:Resmi Charalel/2007-3-15

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(Task 1)
(Task 1)
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==Task 1==
==Task 1==
*Manual analysis of provided sequence:  CACCCTCGCCAGTTACGAGCTGCCGAGCCGCTTCCTAGGCTCTCTGCGAATACGGACACGCATGCCACCCACAACAACTTTTTAAAAGAATCAGAC GTGTGAAGGATTCTATTCGAATTACTTCTGCTCTCTGCTTTTATCACTTCACTGTGGGTCTGGGCGCGGGCTTTCTGCCAGCTCCGCGGACGCTGCC TTCGTCCAGCCGCAGAGGCCCCGCGGTCAGGGTCCCGCGTGCGGGGTACCGGGGGCAGAACCAGCGCGTGACCGGGGTCCGCGGTGCCGCAACG CCCCGGGTCTGCGCAGAGGCCCCTGCAGTCCCTGCCCGGCCCAGTCCGAGCTTCCCGGGCGGGCCCCCAGTCCGGCGATTTGCAGGAACTTTCCC CGGCGCTCCCACGCGAAGC  
*Manual analysis of provided sequence:  CACCCTCGCCAGTTACGAGCTGCCGAGCCGCTTCCTAGGCTCTCTGCGAATACGGACACGCATGCCACCCACAACAACTTTTTAAAAGAATCAGAC GTGTGAAGGATTCTATTCGAATTACTTCTGCTCTCTGCTTTTATCACTTCACTGTGGGTCTGGGCGCGGGCTTTCTGCCAGCTCCGCGGACGCTGCC TTCGTCCAGCCGCAGAGGCCCCGCGGTCAGGGTCCCGCGTGCGGGGTACCGGGGGCAGAACCAGCGCGTGACCGGGGTCCGCGGTGCCGCAACG CCCCGGGTCTGCGCAGAGGCCCCTGCAGTCCCTGCCCGGCCCAGTCCGAGCTTCCCGGGCGGGCCCCCAGTCCGGCGATTTGCAGGAACTTTCCC CGGCGCTCCCACGCGAAGC  
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**This sequence corresponds to Homo sapiens chromosome 10 genomic contig, reference assembly and contains a 1bp point mutation (G to A) at position 201 of the given sequence, which corresponds to position 42969070 in reference sequence.
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**Results from BLAST: 
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**The consequences of this mutation are that...
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***NT_030059.12, Homo sapiens chromosome 10 genomic contig, reference assembly; NW_924884.1, Homo sapiens chromosome 10 genomic contig, alternate assembly (based on Celera assembly)
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***3895 bp at 5' side: hypothetical protein; 425 bp at 3' side: HtrA serine peptidase 1
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***BLAST also revealed a 1bp point mutation (G to A) at position 201 of the given sequence
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**There is an ATG beginning at position 62.  Thus, the mutation mentioned above would cause a CGG to CAG mutation causing an arginine to change into glutamine.  However, since both of these amino acids are polar and hydrophilic.
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**Thus, this particular mutation probably causes no major effect.  Furthermore, since this region of the genome was not annotated to any specific disease, it is probably safe for a physician to reassure the patient that they are perfectly healthy and recommend no change in their lifestyle.
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*Outline of what I did and potential implementation in Python:
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**Ran sequence through Megablast -> connect to known database of all human (and potentially other organisms if needed) sequences and look for matches
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**Searched through BLAST results to identify and assess any mutations between the given sequence and the reference sequence -> search for mutations in the given sequence using methods developed for previous assignments and determine whether changes are major
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**Search OMIM for any relationship to annotated disease alleles -> connect to OMIM and search for matches to given sequence
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**Determined consequences of mutations -> if major change and disease allele - then recommend consulting a physician; otherwise, say that person is probably fine.  
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==Task 2==

Revision as of 22:50, 14 March 2007

Task 1

  • Manual analysis of provided sequence: CACCCTCGCCAGTTACGAGCTGCCGAGCCGCTTCCTAGGCTCTCTGCGAATACGGACACGCATGCCACCCACAACAACTTTTTAAAAGAATCAGAC GTGTGAAGGATTCTATTCGAATTACTTCTGCTCTCTGCTTTTATCACTTCACTGTGGGTCTGGGCGCGGGCTTTCTGCCAGCTCCGCGGACGCTGCC TTCGTCCAGCCGCAGAGGCCCCGCGGTCAGGGTCCCGCGTGCGGGGTACCGGGGGCAGAACCAGCGCGTGACCGGGGTCCGCGGTGCCGCAACG CCCCGGGTCTGCGCAGAGGCCCCTGCAGTCCCTGCCCGGCCCAGTCCGAGCTTCCCGGGCGGGCCCCCAGTCCGGCGATTTGCAGGAACTTTCCC CGGCGCTCCCACGCGAAGC
    • Results from BLAST:
      • NT_030059.12, Homo sapiens chromosome 10 genomic contig, reference assembly; NW_924884.1, Homo sapiens chromosome 10 genomic contig, alternate assembly (based on Celera assembly)
      • 3895 bp at 5' side: hypothetical protein; 425 bp at 3' side: HtrA serine peptidase 1
      • BLAST also revealed a 1bp point mutation (G to A) at position 201 of the given sequence.
    • There is an ATG beginning at position 62. Thus, the mutation mentioned above would cause a CGG to CAG mutation causing an arginine to change into glutamine. However, since both of these amino acids are polar and hydrophilic.
    • Thus, this particular mutation probably causes no major effect. Furthermore, since this region of the genome was not annotated to any specific disease, it is probably safe for a physician to reassure the patient that they are perfectly healthy and recommend no change in their lifestyle.
  • Outline of what I did and potential implementation in Python:
    • Ran sequence through Megablast -> connect to known database of all human (and potentially other organisms if needed) sequences and look for matches
    • Searched through BLAST results to identify and assess any mutations between the given sequence and the reference sequence -> search for mutations in the given sequence using methods developed for previous assignments and determine whether changes are major
    • Search OMIM for any relationship to annotated disease alleles -> connect to OMIM and search for matches to given sequence
    • Determined consequences of mutations -> if major change and disease allele - then recommend consulting a physician; otherwise, say that person is probably fine.

Task 2

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