BIOL_A108 Module 2 Bioinformatics Exercise: Sequence Alignment LAB25 pts. Individual, due week 8 W/Th. in lab. You can collaborate with your group.Name: Section/TA:1. (25pts.) Sequence search by alignment (BLAST). You designed primers targeting a human mitochondrial gene (COX1) and you run PCR on ancient DNA found in a paleolithic cave in France. You see a 700bp amplicon on gel electrophoresis. This is the Sanger DNA sequence of your 700bp PCR amplicon:>MY_CAVE_DNA_SEQUENCE_700bpATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGGAACACTATACCTACTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCCGAACTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGGGGCTTTGGCAACTGACTAGTTCCCTTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAATATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGCTCGCATCTGCTATAGTGGAAGCCGGCGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATTAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCCCTTTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAGTACCTATT(a) What organism do you expect your sequence to be from? Why? Why might it actually be the DNA of another organism?(b) BLAST your sequence at NCBI BLAST to search against all possible DNA sequences reported. Input your sequence (query) with Parameters: Database standard (nr/nt) – to try all sequences as subjects (unbiased), and Optimize for: Somewhat similar sequences (blastn) – to allow for mismatches. BLAST is at the link: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn
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