Bioinformatics Homework 1

Bioinformatics Homework 1 - CS 167/290D Homework #1, Due...

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CS 167/290D – Homework #1, Due October 25, midnight NCBI: http://www.ncbi.nlm.nih.gov/ EXPASY TOOLS: http://us.expasy.org/tools/ PDB: http://www.rcsb.org/pdb/ SIM: http://web.expasy.org/sim/sim.html Problem 1: (12 points) 1. What is the complimentary sequence to the following string of nucleotides? Be sure to label the 5’ and 3’ ends. 5’- GCATATCGTAATGCCATA – 3’ 2. What is the expected number of times you would find the above sequence on chromosome Y in H. sapiens by chance? Assume that the occurrence of each nucleotide is independent and incorporate the prior expectation of each symbol's occurrence on chromosome Y ( NCBI Reference Sequence: NC_000024.7 ). Report the empirical probabilities you obtain. 3. What is the actual number of times that this sequence occurs on chromosome Y? 4. Show the mRNA transcript for the above sequence and the final protein sequence. Note that the template strand for transcription is the 3’ to 5’ strand running anti-parallel to the above strand. Problem 2: (8 points) Find the DNA sequence of alpha globin gene from NCBI webpage by searching across the nucleotide database for gene id 28548. Examine the introns and exons of the gene. 1. At which positions are the translation initiation and termination codons in the gene?
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Bioinformatics Homework 1 - CS 167/290D Homework #1, Due...

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