Academic Writing

Zamknięty Opublikowano May 16, 2014 Płatność przy odbiorze
Zamknięty

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 [url removed, login to view]

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

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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 [url removed, login to view] as input and

Pisanie artykułów popularnonaukowych

Numer ID Projektu: #5947453

O projekcie

3 ofert Zdalny projekt Aktywny Jun 22, 2014

3 freelancerów złożyło ofertę na średnią kwotę $12/godzinę w tym projekcie

alibutt2014

A+ WRITER HERE ----- Ready to start this work, expect HIGH QUALITY from me. Looking Forward.....Thank you!

$12 USD / godzina
(102 Oceny)
6.4
crispwriter

A proposal has not yet been provided

$15 USD / godzina
(25 Oceny)
4.9
vision3080

Hi, I am a professional writer & have a native team. I have been working on Elence/oDesk for 2 years. I can handle this project easily. Please give me chance to prove me. Don't worry about quality & deadline. I am eag Więcej

$8 USD / godzina
(0 Oceny)
0.0