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