These free exercises use the open-source modules of the Cybertory^TM Virtual Molecular Biology Laboratory platform. Please contact us if you would like to install the programs and data sets on your own server. Using your own server may be more reliable for classroon use.

• Shotgun Sequencing
• HIV Genotyping
• PCR Primer Design
• Paternity
• Forensics
• Computerized STR Analysis
• Virus Identification currently under (re)construction

• Shotgun Objectives Evaluation
• Shotgun Pre/post Test
• This exercise uses the Staden sequence data management package to assemble simulated experimental sequence traces from an 8.5 kb fragment of an HIV virus genome. (The instructions focus on the 2003 Windows version.)
• The protocol describes the experimental procedure for this exercise.
• Traces from the first 25 clones
have already been simulated using forward and reverse universal primers. The zip file also contains the Pregap4 configuration file "config.pg4" to assemble these traces. (old version, assembled sequences)
• Use the sequence trace generator to run additional simulated sequencing reactions to finish the assembly and resolve ambiguities.
• Upload and download your experimental files to share with your classmates.
• A data flow diagram for virtual sequencing experiments is available in SVG format.
• Here is documentation on some problems with assembly users have encountered.

• HIV Objectives Evaluation
• HIV Pre/post Test
• This PowerPoint presentation reviews HIV biology and issues related to sequencing.
• Read the protocol, which includes learning objectives and study guide questions . (The protocol is also available in Microsoft Word format.
• The trace subtraction mutation detection technique is described on the Staden website.
• The pregap4 configuration file and HXB2 reference sequence are in zip archive.
• Find the treatment history for your HIV variant from the clone catalog.
• Use these primers to sequence regions of the protease and polymerase genes in the sequence trace generator.
• Reformat the Gap4 mutation report for sending to the HIVdb.
• Find the drug resistances of your virus at the Stanford HIV Database.

• Study the E. coli reference genome.
• Design primers to amplify your favorite gene using the Cybertory PCR simulator on simulated bacteria. Try your primers on other bacteria as well.

• Read the protocol.
• Use the Cybertory PCR simulator on simulated individual humans.
• The simulated family (Pt04-Pt09) is described in this family tree.

• Read the protocol.
• See the expected product sizes and example results on our STR primers page. This information will let you design custom size markers so you can quantitate the number of repeats in each allele.
• STR information is taken from the Short Tandem Repeat DNA Internet DataBase.
• Use the Cybertory PCR simulator on simulated individual humans.
• Search for matching suspects and samples from unsolved crimes using the Cybertory On-line DNA Index System.

• Download and install Genographer
• See the protocol for more details.