Homework 3 – Biomolecules PDF

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Evaluating biomolecule chains in matlab...

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HOMEWORK 3 – BIOMOLECULES (MATLAB): A) Define two sequences in MATLAB: seq_1=’WYLGKLTRMDAEVLLKKPTVRDGHFLVTOCESSPGEFSISVRFGDSVQHHFK VHFKVLRDQNGKYYLWAVKFFNSLNELVAYHRTASVSRTHTILISDMNVSD’ seq_2=’KIRESERWYPGKITRESERLLLNPENPRGTFLVRESETTKGAYCLSVSDFDNA KSLNVKHYKIRKLDSGGFYITSRTQFSSSLQQLVAYYSKHADGLCHRLTN' 1) Use MATLAB to calculate the identity-based score: sum(seq_1==seq_2) ans = 3 identity_based_score=(sum(seq_1==seq_2))*10 identity_based_score= 30 2) Use shuffle to evaluate the score you got in the previous question a) Shuffle one sequence seq_1_1=‘SVSRTHMNVSDTILISDWYLGTVSLNELVAYHRTARDGHFLVTOCE SSPGEFSISVRFGDSVQHHFKVHFKVLRKLTRMDAEVLLKKPDQNGKYYLWA VKFFN’ b) Calculate the new identity-based score sum(seq_1_1==seq_2) ans= 7 c) Repeat to create a histogram of score distributions d) Decide how many repetitions you need to create a reliable histogram shuffle seq_1 5 times shuffle seq_2 5 times ten repetitions e) Compare the score in 1 to the histogram created. Is it significant? The score in one is not significant; the scores from the histogram I created with the shuffled sequences had much higher matches. It was outside of the norm, but on the lower side. So, I would not call it significant.

3) Compare three random protein sequences of length 100, and three pairs length 200. Show the histogram for the pairs. Are there any trends? protein1=’edtfryghjbknlhugybknliohugyftdrtxfcgvjhbknlhiouyuyfghjvbkgyufktkbkhjkhj khjkjlhgfdrtyuqasdjhuftufkghu’ protein2=’srsxqwertyuioplkjhgfdsazxcvbnmljhgfdsatjdjshsaoqknaxoajodjoahoahfoahv ohcoasjocajofhcsuhfugvgddjhdfkk’ protein3=’mkiujnbhytgvcfredxzswqaploikujyhtgrhhfedwsqazaxscdvfbgnhmjmiunybtvr cexwzqpodhsisiowhdkdshdidjsshjdsd’ sum(protein1==protein2==protein3) ans= 0 3 0 0 1 1 0 0 0 protein4=’mkiujnbhytgvcfredxzswqaploikujyhtgrhhfedwsqazaxscdvfbgnhmjmiunybtvr cexwzqpodhsisiowhdkdshdidjsshjdsdsrsxqwertyuioplkjhgfdsazxcvbnmljhgfdsatjdjshsao qknaxoajodjoahoahfoahvohcoasjocajofhcsuhfugvgddjhdfkk’ protein5=’edtfryghjbknlhugybknliohugyftdrtxfcgvjhbknlhiouyuyfghjvbkgyufktkbkhjkhj khjkjlhgfdrtyuqasdjhuftufkghumkiujnbhytglllvcfredxzswqaploikujyhtgrhhfedwsqazaxs cdvfbgnhmjmiunybhvohcoasjocajofhcsuhfugvgddjhdfkk’ protein6=’srsxqwertyuioplkjhgfdsazxcvbnmljhgfdsatjdjshsaolllqknaxoajodjoahoahfoah vohcoasjocajofhcsuhfugvgddjhdfkkhvohcoasjocajofhcsuhfugvgddjhdfkkedtfryghjbknlh ugybknliohugyftdrtxfcgvjhbknlhiouyuyfghjvbkgyufkkhj’

I started part three after I finished the rest of the assignment, and couldn’t get my code to work properly. My computer restarted so I lost what I had and cannot show it. This is all I have to turn in, but I am still going to try to finish it to prepare for the rest of the class....