instructions For this assignment you should implement a program in Perl that solves a bioinformatics problem. The problem is described in the section Problem description below. For this assignment you need to provide the following things: • A rough outline that clearly shows how the problem can be broken down into subproblems (3 p) • Pseudo code that describes how the problem can be implemented (4 p) • A Perl program that implements the program according to the instructions given and that produces the requested output (7 p) • In a written report explain how you solved the problem (implementation) (6 p) More details regarding these requirements can be found further down in the instructions. You will also find a grading template for the different parts. Be sure you study this carefully. Problem description
First you should download the file TNF_protein.txt
This file contains information about the human protein Tumour necrosis factor (TNF) in the database GenBank. From this file you should extract and present the following information: Part 1: the accession number, definition of the protein and organism. Part 2: the protein sequence (all amino acids). The extracted information should be saved in a text file, which is also presented in a userfriendly way. That is, the information should be extracted from the rows with irrelevant information removed. This means that an entire row should not be stored without any processing. Only the requested data specified above should be in the results file. Rough outline For this assignment, a rough outline should be made for Part 2 of the assignment. The rough outline should contain input and output information, all required intermediate steps and contain at least three levels (including top box) at some part in the outline. That is, not all parts are required to be represented with three levels, but where it is suitable it should be included. The rough outline shall be described and clearly explained, so it will be easy to understand. Pseudo code For this assignment, pseudo code should be made for Part 2 of the assignment and build upon the rough outline. The pseudo code should follow some accepted standard and be consistent. It should include all parts listed in the problem description. The pseudo code shall be complemented with explanations, so it will be easy to understand.
Implementation Based on the described requirements, make an implementation of Part 1 and 2 in Perl. In the Perl program, explanations should be provided as comments where it is suitable. The Perl program as well as the output from it must be provided in the submission. Written report The approach taken to solve the problem shall be explained in a written report (Wordformat). In the report, clearly describe in text how the problem was addressed and implemented. The report should include both a general overview on how the problem(s) were implemented as well as describe details about chosen variables, subroutines/functions and how the results were stored