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BioQUEST/bioinformatics or Biology Student Workbench
Off-site linksóthose that require an Internet connectionóare highlighted (e.g., BioQUEST.org).
This exercise is also available from the author at the GenWeb site.
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There are three parts to this assignment.
1. Use electronic PCR to identify STS on large segments
of human genomic DNA.
2. Use these STS to generate a map of this region of the genome
3. Combine overlapping segments to form a contig
Above are links to four segments of human genomic DNA .
Open each page individually. Select and copy the DNA sequence on that page.
Under Electronic PCR select "New Version".
Paste the DNA sequence into the box and select "Submit Query".
Record the names and positions of the STS markers found on each segment of DNA.
Did all of the
segments of DNA contain and STS?
Did some STS appear on more than one segment of DNA?
Once you have used the electronic PCR program to identify the STSs present on each segment of DNA, look for common STS present on different segments.
Use the position of these STSs to draw a map of each segment of DNA.
Did any of the
DNA segments overlap with each other?
Did all of the DNA segments overlap with each other?
Combine any overlapping segments into a contig.
This can be done using a sequence editor if you have one on your computer. If not you can use a word processing program.
To use a word processor, copy segment 1 and paste it into the word processor. Hit return 2-3 times to give space between sequences.
Copy segment 2, which overlaps with segment 1, and paste it into the word processor.
Go up to segment 1 and copy the last 10-20 bp of sequence.
Use the "Find" function on the word processor to find that same sequence in segment 2.
At the end of the common sequence in segment 2 hit return 2-3 times. This separates the overlapping sequence in segment 2 from the non-overlapping sequence.
Now select and delete the region of segment 2 that overlapped with segment 1.
Delete any spaces and returns between segment 1 and segment 2. This generates a longer contiguous segement of DNA (a contig).
Repeat this process with the other segments.
What would have happened if we had not removed
Use the intron/exon splice
site identification program to look for the presence of any genes in