About human HOXD13 (genetics), protein sequence alignment, protein sequencing. Orthologues and paralogues

Question

1. Construct a multiple protein sequence alignment using human HOXD13 and 9 other orthologues of human HOXD13. 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 HOXD13 [5 marks]
2. In FASTA format, download the following Human protein sequences for HOXA13, 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 1 [5 marks]

Answer 1

1) For this, a) You could find a database on orthologs in NCBI b) download FASTA sequence of HOXD3 gene for each of the species that you have chosen c) carry on multiple sequence alignment (MSA) using a suitable tool (such as T-coffee) d) label the figure as asked on your MSA output e) find out which of the species are orthologs and which of them are paralogs.

2) This is very similar to 1. You need to do the similar steps such as retrieving the sequence in fasta format, carrying out MSA, and look at output and describe how these genes are conserved during the evolutionary process.

I hope this is clear. These two questions require some hands on skills to play with sequences and tools.