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BI2234: Molecular Biology Of The Gene - Biology Assignment Help
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Assignment Task: Task 1: Q: Why does CAP3 generate more than 1 contig and/or why are there one or more sequence files (singletons) that are not incorporated into the contig? A: CAP3 finds overlaps between the ends of sequence reads. If a sequence is trimmed excessively then potentially overlapping regions may be removed. Conversely, insufficient trimming may have led to retention of low quality sequence that consequently cannot be aligned. So, for example, if there is an unincorporated sequence (a singleton) you should recheck that both it and the sequences at each end of the contig have been processed appropriately Task 2. Q: The sequences from sea bass and from E. coioides are extensively aligned, but the alignment doesn’t show any obvious introns / why do the introns seem very small? A: Introns below 50 bp are very rare (the smallest known human intron is 30 bp, the largest is over one million bp), typically in vertebrates they are hundreds or thousands of nucleotides in length. If you cannot see putative introns in this size range, then it may be that the wrong sequence from the BLAST hits has been used – remember the correct sequence is from the E. coioides mRNA (used because it lacks introns). Recall also that introns are sequences that intervene with ina gene. Q: The alignment shows little or no similarity between my contig and the E. coioides mRNA. A: Make sure the sequences being aligned are in the same orientation. Task 3 Q: What is meant by “assess the accuracy of the annotation”? A: Inspect the gene via the browser and try to determine whether it’s organisation as shown on the browser is correct. In particular, pay attention to exon-intron boundaries (errors made in assigning these will lead to errors in the sequence of the mRNA, and likely protein, predicted to arise from the gene). Task 4 Q: How do I find the location of the domain on my sequence alignment? A: A protein domain is a distinct structural and/or functional module within a protein - it may include a number of secondary structural motifs (a zinc finger for example contains both alpha helix and beta sheet) and may be quite large. The location of a domain within the input sequence can be found from the results of a conserved domain search in several ways, for example by clicking on either “specific hits”, which generates an alignment that includes the search sequence, or from “Zoom to residue level”. These are indicated by the red arrows in the example below (showing the result of a domain search with the sea bass splicing factor SRSF1). Task 5 The instructions state “and find first the two disease-associated mutations within the exon”, but there are more than two such mutations. What should I do? A: Apologies, this is a typo, the text should read “and find the first two disease-associated mutations within the exon” Task 6 What is the starting point (e.g. should I assume the gene has already been cloned etc)? A: Start from scratch, as a researcher would have to. Assume that you have available tissues and larvae from sea bass and begin from there.This Biology Assignment has been solved by our Biology experts at My Uni Paper. Our Assignment Writing Experts are efficient to provide a fresh solution to this question. We are serving more than 10000+ Students in Australia, UK & US by helping them to score HD in their academics. Our Experts are well trained to follow all marking rubrics & referencing style.