Harvard:Biophysics 101/2007/Notebook:Resmi Charalel/2007-3-15: Difference between revisions
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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 | ||
** | **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== | |||
Revision as of 19:50, 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.
- Results from BLAST:
- 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.
