BIF604 GDB 1 Solution and Discussion

[zareen]

Bioinformatics Computing-II (BIF604)
Assignment No.01
Total Marks 15
Note: There are two questions. First one is theoretical and second one is practical. You are supposed to do your assignment by yourself. Any kind of plagiarism will be marked straight zero.
Question 1: What you have learnt in basics of Bioinformatics. Also enlist and discuss the tools software and methods you have studied till now. (5)
Question 2: Select a raw data set of Arabidopsis thaliana from GEO. Put it into GALAXY and de-contaminate it. After filtering you are supposed to align it on the any of the prescribed reference and show the results (At least header). (10)
The result of every step must be shown in the assignment

In case of any query please email at bif604@vu.edu.pk or contact me on Skype mjhasnain_1 before the deadline (10-11-2019). Please note that you are given with almost 4 weeks. So, no extra time will be granted. You are supposed to do your assignment before the deadline to avoid several issues like unavailability of internet, electricity and signals etc.

[zareen]

@zareen said in BIF604 Assignment 1 Solution and Discussion:

What you have learnt in basics of Bioinformatics. Also enlist and discuss the tools software and methods you have studied till now.

Sample Assignment
1-Go to the NCBI database

Open NCBI

Select Protein database from here

Enter the name of your candidate gene (a gene, which you want to work upon)

Enter the name of your candidate gene (a gene, which you want to work upon) Enter it-> it will give you a list of all possible sequence datasets available related to the your gene (protein)

Open it and then you can see the full sequence with all desired information in the first line.

Click on the BLAST icon present at the top of right menu ORyou can copy the sequence and open BLAST -> Protein to Protein (blastp) and past the sequence in input section.


Then select Protein date bank database as reference

Then Click on the BLAST Icon

It might take some seconds

It will show a page like this

At the lower part of the pageyou will see a list of reference sequence of protein structure which our sequence has been mapped upon. Where at the right side different columns are giving the information about the identity, Query coverage and Accession ID etc

At the lower part of the pageyou will see a list of reference sequence of protein structure which our sequence has been mapped upon. Where at the right side different columns are giving the information about the identity, Query coverage and Accession ID etc From here click the Accession IDs of top three references one by one and It will lead you to the following page for each time for each reference.

From here get the Complete information like accession number, Locus, Coding region etc. of the three references one by one and make a table. Then go back to the first page where you found your first sequence from.

From the above page see the right top encircled area it will give you the information about the orthologs of the Human Gene. Past the sequences of the same genes extracted from those three orthologs. At the end enlist all the databases tools software which you will have used.