Assessment 1
Answer all questions in a separate word document. Completed assessments paper will be submitted into Turnitin. All questions can be completed by information and links found in the online databases and tools discussed in online Practical Class 1.
SIT111 Truth Table To Canonical Representation Assignment-Deakin University Australia.
1.Provide a short description of the function of HOXD 13
2.Using the FASTA format of the HOXD 13 transcript, translate the three forward frames of the transcript. What is the correct reading frame (Frame 1, 2 or 3) [1 mark]? In your report, paste a FAST A format of the translated HOXD 13 protein, and in the figure legend indicate the number of amino acids in the HOXD 13 protein, the total length of the Homo sapiens HOXD 13 mRNA transcript, the nucleotide accession number for this transcript, and the number of 5’ and 3’ nucleo tides that are not translated
3.Construct a multiple protein sequence alignment using human HOXD 13 and 9 other or thologues of human HOXD 13. In the figure legend, describe what is being shown,and specify the size (start and stop number of amino acid) and location of conserved domain(s) in HOXD 13
4.In FAST A format, download the following Human protein sequences for HOXA 13,HOXB13, HOXC13, HOXD13; using the ALIGN function in UniProt, generate a multiple protein sequence alignment. In the figure legend, describe what is being shown (orthologues or paralogues?), and comment on DNA conservation, including a comparison with the alignment presented in question 3
SIT111 Truth Table To Canonical Representation Assignment-Deakin University Australia.
5.In a table, identify and list 5 mutations in human HOXD13 that have clinically relevant phenotypes. Individual columns need to 1) Identify the position of the mutation (amino acid number and change); Identify the type of mutation (missense, nonsense,frame shift etc.); the likely effect of the mutation on protein function; the clinical phenotype of the mutation
The FASTA sequence and multiple sequence alignments (questions 2-4) are figures and must have figure legends. A figure legend begins with a short descriptive title (e.g. Figure 1. Multiple Alignment of 5 HOX Proteins) and then provides a description of what the figure is showing. The Table in question 5 has a title at the top of the table – it does not have a legend.
Additional Information
Manually download and align protein sequences (Question 4)
FASTA
When manually downloading FASTA protein sequences for a multiple sequence alignment, you will see that the first one to two lines are descriptive, for example, below is the FASTA description of HOXD13:
>sp|P35453|HXD13_HUMAN Homeo box protein Hox-D13 OS=Homo sapiens OX=9606 GN=HOXD13 PE=1 SV=3
Before starting the multiple sequence alignment for manually downloaded sequences in question 4, simplify the first line of the FASTA formatted sequence to:
>HXD13
Note that the ”>” is required
Describing a mutation
Mutations are described by their location and the change made by the mutation. Use the information below when completing the table for Question 5
Table taken from: Journal of Molecular Diagnostics, Vol. 9, No. 1, February 2007© American Society for Investigative Pathology and the Association for Molecular Pathology
Structure and naming of amino acids
SIT111 Truth Table To Canonical Representation Assignment-Deakin University Australia.
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