Academic Writing

Biopython/python project Pipeline: Basic Python File Manipulation and BioPython: Seq Object (15 Marks) A DNA sequence has been provided in a file called nucleotide_sequence.txt. a) Open and read the contents of the text files. Print this sequence to the screen. 3 Marks b) Create a DNA Seq object using the sequence that was read from the file in part a. 4 Marks c) Translate this nucleotide sequence to a protein sequence called protein_sequence. 8 Marks BioPython: BLAST Record Manipulation and Visualisation The sequence from Q1 must be identified as follows (A BLAST UML diagram has been provided for your reference): (55 marks) a) Run a BLAST on the unidentified protein sequence and save the results as an xml file called betp.xml. 5 Marks b) Open the BLAST output and read the records into a list. 5 Marks c) Use for loops and if statements to process the BLAST hits to print the description title of the BLAST hit with the highest score. You should find that the highest score is 3083 and the protein is betP, a membrane bound transformer protein. 30 Marks d) You would like to visualise the scores from the other hits. Create a list of hsp scores from all hits and plot these using the matplotlib library with “BLAST Scores” as the x axis, “# Hits” as the y axis and “Scores pf 50 Blast Hits” as the title. A reference screenshot has been provided. 15 Marks BioPython: SeqRecord, SeqIO and [login to view URL] a) a) Write the protein sequence obtained in Q1 to a fasta file entitled betp_sequence.fasta. The sequence is required to be in SeqRecord format. Parse (30 marks) 22 Marks Page 2 of 3 the description of the best hit obtained in Q2 to retrieve the id, name and description of the sequence which should be as follows: b) c) id = gi|62389782|ref|YP_225184.1 d) name = gi|62389782|ref|YP_225184.1 e) Description = gi|62389782|ref|YP_225184.1|glycine betaine transporter [Corynebacterium glutamicum ATCC 13032] f) g) b) Realign the sequences using MUSCLE. This will take the [login to view URL] as input and