Assignment 3: Sequence Comparison Part 1: Running BLAST Step 1: - - PowerPoint PPT Presentation

Assignment 3: Sequence Comparison

Part 1: Running BLAST

Step 1: Obtain Gene Sequence

• Obtain coding sequence for RAP1 from yeastgenome.org

Step 1: Obtain Gene Sequence

Step 2: Run BLASTx Web Tool

• Compare BLOSUM62 vs. BLOSUM80
• Compare default existence (11), extension (1) penalties vs existence of 7,

extension of 2

Step 2: Run BLASTx Web Tool

Step 2: Run BLASTx Web Tool

Part 2: Align Reads to Chr22 with Bowtie

Step 1: Create Index for Chr22

• Create an index for chr22 using bowtie2-build
• Example command in assignment

Step 2: Align with Bowtie

Step 2: Align with Bowtie

• Align reads in reads.fq file

○ (provided in /home/assignments/assignment3)

• Things to note for running bowtie

○ reads.fq contains unpaired reads ○ alignment output should be saved to a file ○ report output should also be saved to a file

Step 3: Compare (Di)Nucleotide Frequencies

• Compare nucleotide, dinucleotide frequencies for reads.fq and chr22

○ Look at enrichment of reads.fq nucleotides, dinucleotides compared to chr22

• Use nuc_count_FINAL.py to get frequencies

○ (provided in /home/assignments/assignment3)

• Do NOT need to edit this script, only run it on each file

What To Turn In

• Completed README.txt
• Bowtie alignment file
• Bowtie report file

Extra Credit

Extra Credit

• Run BLAST on the class server
• Identify unknown species using unknown.fsa

○ (provided in /home/assignments/assignment3)

• Turn in your BLAST output file