BI118G: Bioinformatic Analysis with Perl - IT/Computer Science Assignment Help

Assignment Task:

Instructions

This assignment consists of 3 tasks related to the lecture material. For each task, you should implement a Perl program according to the description. For each task you will get 0-5 points, as follows:

• 0 points if the program is missing, if it is completely wrong or is not executable.

• 1 point if the program contains several major errors.

• 2 points if the program contains some major error or several minor errors, and includes using badly chosen programming constructs.

• 3 points if the program is a reasonable attempt that basically solves the task, but contain some minor errors or badly chosen programming constructs.

• 4 points if the program solves the task and only contains some minor errors.

• 5 points if the program solves the task and contains no errors. For each task you can get additionally 2 points if you include comments that explain statements where a data structure, control structure or regular expression is used. This is an example of a comment that is not sufficient and will not give any extra points: #A variable is used $name = “John”; This is an example of a comment that is sufficient and will give extra points: #The variable named $name is assigned the value “John” $name = “John”; For this assignment it is not allowed to use any external modules or packages. For example, it is not allowed to use modules/packages from BioPerl. Only built-in functions that come as default when installing Perl are allowed.

The maximum score for the assignment is 21 and you get a grade according to this scale: F: 0-11, E: 12-13, D: 14-15, C: 16-17, B: 18-19, A: 20-21 The assignment is solely individual work since it is part of the examination for the course. It is not allowed to cooperate with other students or copy code from other students or any other type of source when you answer the questions. Any undue actions will lead to fail (grade F) and may be reported to the Disciplinary Committee, depending on how severe the actions are. In case you fail the assignment (grade F), you will have one opportunity for reexamination. In that case you will get a new set of questions and approximately one week to solve the tasks. If you fail a second time, then you will need to wait until the next time the course is given to get a new chance. Your programs must be uploaded in the assignments section of the course site. You need to make a compressed archive of the Perl program files, where each program file has the suffix .pl, and upload the zip-file as your submission, or you upload each Perl program separately. Programs that are not in .pl-format will not be accepted.

1. Download the file sequence.gp.txt from Canvas, which is a text file containing an entry from Genbank protein sequence database. Write a program that extracts the following information from the file:

• Locus ID

• Number of amino acids

• Amino acid sequence with capital letters The extracted information should be printed to a results file and should only contain the requested information, i.e., any space characters or other characters surrounding the information should be removed before printing. Hence, it is not allowed, e.g., to print one entire row from the file without any processing. The program should be generic, so it is possible to change the Genbank file to another one.

2. Download the file sequence.gp.txt from Canvas, which is a text file containing an entry from Genbank protein sequence database. Write a program that includes a subroutine, where the subroutine takes as input argument the content of the file and returns all keywords (KEYWORDS) from the file. In the return argument only the keywords should be included and nothing else. The program should be generic, so it is possible to change the Genbank file to another one. Print out the keywords to terminal window.

3. Download the file GeneExpressions.txt from Canvas, read in the content from the file and store it in a 2D array. The file contains expression values for four genes (GeneID) during three time points (Tp). Thereafter, calculate the sum of expression values for each gene and print out the information in the terminal window including an informative message.

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