There are two questions: Spider Silk and an unknown.
Question #1 Spider Silk (14 points)
In this problem set, you will be analyzing a silk gene and protein.
1a. Retrieve the protein sequence record of the full length major ampullate spidroin 1 protein for the western black widow spider, cloned by Ayoub and co-workers.
1b. Examine this sequence by eye. Do you see a pattern? Introduce or remove carriage returns into a FASTA file to visually present this pattern to the reader. Paste this newly formatted sequence into your document.
1c. Describe the pattern you identified in 1b, above.
1d. Using the PIR Composition/Molecular Weight Calculation Form, determine the composition of the major ampullate spidroin 1 protein. From the results page, paste in a screenshot of the sequence field (including the coordinate numbering along the left side of each line) PLUS a second screenshot of the composition graph into your document. Discuss/compare the result to the amino acid composition of the entire Swiss-Prot database (On one of the slides from lecture 8, Tools).
1e. Using the NCBI ORF Finder Web form, determine the open reading frames for the entire DNA record for this protein (coding region plus flank). Paste in a screenshot of the ORF Finder graphics into your document. Based on what you see in the screenshot, describe your choice of the correct reading frame and why you made that choice. Discuss your other strong choice. Besides the annotation and published amino acid sequence for this protein, how might you (bioinformatically) rule out this second reading frame as a source of silk protein? Or could it be another silk protein? Present your arguments, for and against.
1f. Examine the codon usage of the correct reading frame by using the Codon Usage tool from the Sequence Manipulation Suite. Yes, this is a tool not covered in class. But we have covered the concepts. Discuss the highlights and how they relate to what you know about this gene and protein. Paste a screenshot of the relevant results into your document.

Question #2 What is it? (10 points)
>Unknown-PS#4-2019
MALFTKSSSSVAVTDKDTFELSTFLESSKAPQHDRDELPEQRSVGGGLDV
PLRPVGFGG

There are two questions: Spider Silk and an unknown. Question #1 S...