Assignment 4

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1. What is CIGAR string? How is it generated and where will you find it?

2. What is BAI file and how is it made? Be specific?

3. Compare and contrast FASTA and FASTQ files

4. What is the relationship between SAM,BAM, and BAI? how is each of these generated? What information do they contain and why are they useful?

5. Using pseudocode, describe an algorithm that searches for all instances of ATC in a given sequence. What do you think the BigO will be for this algorithm and why?

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