BIT150 – Fall 2008 –
Homework 4 KEY
Due on Thursday October 23th by email to TA: [email protected] as
Hwk4_Lastname BEFORE the Lab
1. 20 points Using Pregap4 and Gap4, assemble the 21 sequences that are part of
Triticum monococcum L. BAC clone 322N9.
In the ‘Configure Modules’ tab of Pregap4:
General Configuration: For Get entry names from trace files, select No.
Estimate Base Accuracies: Select Logarithmic (Phred) scale.
Trace Format Conversion: Leave default parameters.
Initialize Experiment Files: You cannot modify it.
Augment Experiment Files: Do not add any extra information.
Quality Clip: Leave default parameters.
Sequencing Vector Clip: In Select Vector-primer subset, select pBS/HindIII.
Screen for Unclipped Vector Clip: OK.
Cloning Vector Clip: Unselect this option.
Gap4 Shotgun Assembly: In Gap4 database name, put a name for your output, and
make sure you change the version every time you perform a new assembly with
different parameters. Create new database, and RUN.
Answer the following questions:
ANSWERS
- According to the database information:
1.1. Were all the sequences provided used to perform the assembly?
Yes. The 21 sequences were used to perform the assembly.
1.2. How many contigs were created? How many sequences were included in
each contig? What is the length (bp) of each contig?
2 contigs were created. The larger contig included 20 sequences, and had a
length of 3,600 bp, and the smaller contig included 1 sequence, and had a length
of 54 bp.
- Look at the confidence values used for the base-calling:
1.3. Present a confidence value graph for all contigs.
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