Exercise 7 - BAC Clone Annotation
BAC clones - Bacterial Artificial Chromosomes - allow the cloning of large nucleotide fragments such as 100 or 200 kb.
These clones are important tools for the sequencing of the genomes of higher organisms. In this exercise annotate your own BAC
clone of 161,250 nucleotides from an ongoing sequencing project at Cold Spring Harbor Laboratory.
BAC clones are subcloned in short fragments of 500-1,000 bp, which can then be sequenced.
Subsequenttly, the sequenced clones are mapped back to the original BAC clone through extensive
finger-printing analysis. The clones are digested, run on gels, trasnferred to Southern Blots and
hybridized against STS-sequence probes. This
image shows an
authentic autoradiograph of a respective mapping project at the University of Washington in St. Louis.
Open the image and identify clones that share identical fragments and, thus, might represent fragments
located adjacently on the original BAC clone.
Annotate your own
genomic clone
utilizing the annotation tools in the list below. Save your results in a word processor,
as entire web pages, and/or as screen shots.
Programs:
Answer the following questions:
- What organism is this clone derived from?
- How do the results change when you change the settings for the annotation tools?
- How many genes do the different programs predict for this clone?
- Identify intron-exon splice sites.
- Identify restriction sites for four different restriction enzymes.
Compare your results here.
Check these two excellent sites for additional information on annotation:
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