Homology-based Methods

Methods: Make sure in your methods section that you state which kind of BLAST you used for each task and explain why. (还要包括fgenesh 和augustus两个database的说明。)
Results: Based on the tasks carried out in the prac on your allocated 20-kb DNA sequence (attachment:) (make sure you note which sequence you worked on), present the findings in this section of the report. Specifically, we are looking for:1. A summary diagram of the gene models from the program you believe represents the best, most accurate ab initio annotation. Provide a summary diagram showing the entire 20kb of DNA annotated with all predicted genes. Your diagram should indicate the base-pair positions of all gene features. You must show exons, introns, start and stop sites and the gene direction. You should also provide the polypeptide sequence encoded by each gene. Include in the text the annotation method you chose to depict in your diagram, and why you chose it (i.e. strengths and weaknesses compared to other methods). Explain the support you obtained for these predictions. Use the appropriate BLAST program to determine the type of protein produced from each gene predicted by your chosen ab initio method. Present the evidence and comment on your confidence in each BLAST result. 
2. Report on the homology-based method to give an independent prediction of the gene models in your 20-kb sequence. Provide a summary diagram showing the entire 20 kb of DNA, annotated with all predicted genes. Your diagram should indicate the base-pair positions of all gene features. You must show exons, introns, start and stop sites and the gene direction. You should also provide the polypeptide sequence encoded by each gene. Determine the type of protein produced by each gene predicted by the homology- based search. Present the evidence and comment on how confident you are in each BLASTx result.3. Find and identify the one type of gene that is found on all DNA fragments for the class. Either download another few sequences to identify the gene type in common, or check with your colleagues which gene types they found.Tip for visualisation purposes: Geneious Prime is very convenient to show annotations along a sequence. You can download a free trial from here: https://www.geneious.com/prime-features (Links to an external site.). Alternatively, visualise the results in PowerPoint or similar software.Discussion: Include the following discussion points:1. Compare the ab initio predictions and the BLASTx-based homology predictions for your sequence and comment on which approach worked best for annotating your sequence. 
2. Comment on why BLASTx was used for the homology-based prediction. How is BLASTx different to the other kinds of BLAST? 
3. Discuss the predicted biological and/or biochemical function of the gene found in Results #3 above. Include the nature of the conserved functional motif(s) and the homology to characterised genes. You will need to search the scientific literature in order to determine the biological and/or biochemical function of the chosen gene.

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