Write a Python script to extract the upstream

Assignment Help Python Programming
Reference no: EM133048534

Your work will be evaluated on four axes:

Scope: The extent to which your code implements the features outlined in the specification.
Correctness: The extent to which your code is consistent with the specification and is free of bugs.
Design: The extent to which your code is well written (i.e. clear, efficient, elegant, logical).
Style: The extent to which your code is readable (i.e. commented, indented, containing aptly named variables and subroutines).

Background:
A gene's 5' flanking region has a major role in defining the timing, location, and level of its expression. These nucleotides include specific patterns typically 5-31 nucleotides long (mean 9.9 nt) that are binding sites for transcription factors that regulate transcript abundance. Identification of these regulatory sequences contributes to an understanding of gene regulation in vivo and contributes to efforts to artificially modulate gene expression. Several studies have identified putative functional regulatory sequences on the basis of their over-abundance in a set of co- regulated genes.

Transcription factors recognize conserved sequences in the promoter region upstream of a gene's transcription start site (TSS). Binding of the transcription factor initiates transcription of the downstream gene (actually, several transcription factors work in combination). If a set of genes share a common expression pattern, it is reasonable to assume that their transcription is activated by the same transcription factors, and that their promoter regions will share transcription factor binding sites (TFBSs). We call these sites "conserved non-coding regions", and because they are conserved we can find them using pattern-matching algorithms.

One strategy is to search promoter sequences for known motifs: i.e. ones that have been reported in the literature and experimentally confirmed to be transcription factor binding sites.

Assignment:
For this assignment I want you to search for known motifs in the upstream promoter regions of a set of coexpressed genes. The file zea_mays_genes.txt contains a list of maize (Zea mays) gene identifiers for a group of co-regulated maize genes. The file promoters contains a list of experimentally identified TFBSs that are active in maize. You will need to:

Obtain a fasta file containing the maize genome, version AGPv4.

You can also use ftp to collect these files.

Obtain GTF/GFF file for the same version to find the TSS for each gene.

Write a Python script to extract the upstream non-coding sequence for each gene in zea_mays_genes.txt. 500nt is a reasonable size for maize promoter regions.

Using the list of known binding motifs in promoters, search for matches in the genes' promoter regions and report the number of times each motif was found.

Perform the same analysis on an equivalent number of randomly selected genes.

Compare the motif counts of the random and selected genes.

Submit any Python scripts that you use to do these tasks, as well as two separate files that list the counts of motifs from the selected genes and the random genes. The first column should be the motif and the second column should be the count, separated by tabs. If some motifs appear to be notably over or under represented amongst the coexpressed genes, please note them in a separate text file.

Hints and warnings:
Using SeqIO from Biopython can make reading in the large chromosome sequences faster, but one can also stick with python.
Be careful. Genes are also encoded on the reverse complement strand.
Some genes have multiple TSSs. Choose the most upstream one.
The promoter motifs sometimes have alternate bases, e.g. [AG]CCGAC means either ACCGAC or GCCGAC.

Consider double-checking that you are extracting the correct promoter sequences: e.g. blast a few of your promoter sequences against the genome and make sure that the positions in the blast output match the expected positions in the GTF/GFF file.

When the maize genome was assembled, missing sequence regions are replaced with a string of 100 Ns, so this pattern represents an unknown length of missing DNA. Be sure that your promoter sequences do not contain these Ns or sequences upstream of the Ns. Use a shorter promoter sequence if this happens.
Make sure to use functions. They can help keep your code clean and readable.
The randomly selected genes can be selected from the gff3 file.
Other than Biopython and re if desired, no modules that are not included with Python should be used.

Attachment:- Assignment.rar

Reference no: EM133048534

Questions Cloud

The importance of business ethics : The system of moral and ethical beliefs that guides the values, behaviors and decisions of a business organization and the individuals within that organization
Positive and negative consequences of power : 1: As a manager for a business company, which type of power is best to incorporate?
Complete the necessary journal entry for interest payment : Complete the necessary journal entry for the interest payment date of June 30, 2019 by selecting the account names
Determine how to minimize the net cost incurred : Determine how to minimize the net cost incurred in meeting the demands for the next four months.
Write a Python script to extract the upstream : Write a Python script to extract the upstream non-coding sequence for each gene in zea_mays_genes.txt. 500nt is a reasonable size for maize promoter regions
How much income will tom recognize : The basis of the property was $45,000 and its fair market value was $75,000. How much income will Tom recognize
What are the tax effects to c corp : B Corp has a basis of 1,000,000 in its shares of C Corp and Irene has a basis of $20,000 in her shares. What are the tax effects to C Corp
What is the concept of budgeting : Question - What is the concept of 'budgeting', its advantages, and how can they be used to measure performance
Combination of types of authentication : What do you think is the best combination of the types of authentication? Is that type of authentication appropriate for all types of access.

Reviews

len3048534

12/16/2021 8:36:53 PM

BIOINFORMATICS PYTHON ASSIGNMENT I have shared the sample so just see sample have idea and use ur idea and make totally The Assingment sample work of my friend Thank you NOTE : The file code 1 contains the assignment done...but its worth is only 60% I have just attached that to get an idea...please don''t copy anything from that its just for ease to get an idea... other files needed are attached... there is an output file also needed... after the code is created for assignment when it runs it should provide output like this I have attached the screenshot. PLEASE FOLLOW THE INSTRUCTIONS AND SEE THE MATERIAL AND DO IT NICELY AND ATTACH US THE TURN IN IN REPORT.

Write a Review

Python Programming Questions & Answers

  Write a python program to implement the diff command

Without using the system() function to call any bash commands, write a python program that will implement a simple version of the diff command.

  Write a program for checking a circle

Write a program for checking a circle program must either print "is a circle: YES" or "is a circle: NO", appropriately.

  Prepare a python program

Prepare a Python program which evaluates how many stuck numbers there are in a range of integers. The range will be input as two command-line arguments.

  Python atm program to enter account number

Write a simple Python ATM program. Ask user to enter their account number, and print their initail balance. (Just make one up). Ask them if they wish to make deposit or withdrawal.

  Python function to calculate two roots

Write a Python function main() to calculate two roots. You must input a,b and c from keyboard, and then print two roots. Suppose the discriminant D= b2-4ac is positive.

  Design program that asks user to enter amount in python

IN Python Design a program that asks the user to enter the amount that he or she has budget in a month. A loop should then prompt the user to enter his or her expenses for the month.

  Write python program which imports three dictionaries

Write a Python program called hours.py which imports three dictionaries, and uses the data in them to calculate how many hours each person has spent in the lab.

  Write python program to create factors of numbers

Write down a python program which takes two numbers and creates the factors of both numbers and displays the greatest common factor.

  Email spam filter

Analyze the emails and predict whether the mail is a spam or not a spam - Create a training file and copy the text of several mails and spams in to it And create a test set identical to the training set but with different examples.

  Improve the readability and structural design of the code

Improve the readability and structural design of the code by improving the function names, variables, and loops, as well as whitespace. Move functions close to related functions or blocks of code related to your organised code.

  Create a simple and responsive gui

Please use primarily PHP or Python to solve the exercise and create a simple and responsive GUI, using HTML, CSS and JavaScript.Do not use a database.

  The program is to print the time

The program is to print the time in seconds that the iterative version takes, the time in seconds that the recursive version takes, and the difference between the times.

Free Assignment Quote

Assured A++ Grade

Get guaranteed satisfaction & time on delivery in every assignment order you paid with us! We ensure premium quality solution document along with free turntin report!

All rights reserved! Copyrights ©2019-2020 ExpertsMind IT Educational Pvt Ltd