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Chapter Two Exercises
1. Edit two sets of overlapping sequence trace files with phred, and merge them into a contig with phrap and consed.
Download the 16 .abi files from below. These files represent two different sequence reads (A and B) in opposite directions from one fragment of the Drosophila genome, from 8 different flies. Each fly was homozygous for the particular gene that was sequenced. The two sequences are from opposite strands, and overlap for about 200 bp at the ends. Consequently, you should be able to make a single contig with 8 different sequences of the gene that differ at a number of polymorphic sites. Make a list of these sites, document the frequencies of the alleles, and compute the consensus sequence.
2. Perform a BLAST search with the consensus sequence derived from Exercise 1.
3. Use Clustal to align the sequences obtained in Exercise 2.
4. Run GenScan on a scaffold sequence containing the full-length gene.
5. Perform a phylogenetic analysis of the aligned sequences in Exercise 3.
Files:
- All files, compressed: traces.zip
- Raw files:
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