Snpfunction

Project Member

Corey Harada

The goal of this quarter

Create a program to analyze a SNP based on the change it makes to the protein coded by the region the SNP lies in.

The Schedule for the quarter

Week 4: Set up wiki page
Week 5: Look at pygr, get sequence from genome.
Week 6: Get exons from genome.
Week 7: Transcribe sequence to protein.
Week 8: Develop method for comparing proteins.
Week 9: Run program on data, analyze
Week 10: Finish analysis

Project Description

This project seeks to find the function of a SNP by looking at how the SNP changes the coding of a protein.

Related Papers

April 21-25 2008

  1. What I did this week: Created wiki page, looked at Pygr
  2. What I plan to do next week: Find a way to go from a SNP to the exon around the SNP to the protein coded by the exon
  3. What you did compared to what you planned to do: I was only required to complete the wiki page.
  4. What grade you think you deserve for your work on the project for the week: A

April 26 - May 2 2008

  1. What I did this week: Found way to get a sequence from the human genome given a location. Searched for databases that hold exon locations.
  2. What I plan to do next week: Find exon locations, start transcribing to protein.
  3. What you did compared to what you planned to do: I did not get as far as I had planned.
  4. What grade do you think you deserve for your work on the project for the week: C

May 3 - May 9 2008

  1. What I did this week: Found databases with gene names, exon locations, and protein names. Started on transcribing sequence to protein.
  2. What I plan to do next week: Finish transcribing sequence to protein.
  3. What you did compared to what you planned to do: I accomplished roughly what I planned.
  4. What grade do you think you deserve for your work on the project for the week: B

May 10 - May 16 2008

  1. What I did this week: Worked more on transcribing sequence to protein.
  2. What I plan to do next week: Finish work on transcribing proteins.
  3. What you did compared to what you planned to do: I did not get as much done as I would have liked due to unforseen difficulties in translating the sequence to protein.
  4. What grade do you think you deserve for your work on the project for the week: C

May 17 - May 23 2008

  1. What I did this week: Finished transcription work, looked at BLAST to compare protein sequences.
  2. What I plan to do next week: Construct a method of scoring proteins based off of BLAST.
  3. What you did compared to what you planned to do: I accomplished what I had planned, though I would have liked to do more with BLAST.
  4. What grade do you think you deserve for your work on the project for the week: B

May 24 - May 30 2008

  1. What I did this week: Created a BLAST score, ran data through BLAST.
  2. What I plan to do next week: Finish.
  3. What you did compared to what you planned to do: I accomplished about what I planned to.
  4. What grade do you think you deserve for your work on the project for the week: B

May 31 - June 6 2008

  1. What I did this week: Looked at analysis of known function snps, worked on presentation, presented.
  2. What I plan to do next week: None
  3. What you did compared to what you planned to do: I finished the project. If there is anything extra I would have liked to do, it would be to find more known SNPs and run the program on them, as well as to work more on improving the algorithm for scoring.
  4. What grade do you think you deserve for your work on the project for the week: B
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