BIF604 Assignment 1 Solution and Discussion


  • Cyberian's Gold

    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 [email protected] 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.


  • Cyberian's Gold

    @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
    11c278ed-e4bc-4217-999d-3a415a59f237-image.png
    Open NCBI
    da54bdc9-515e-4a47-ac88-00186f9509cc-image.png
    Select Protein database from here
    aba43dd4-1739-478e-b3f8-1fcd1fa1ffea-image.png
    Enter the name of your candidate gene (a gene, which you want to work upon)
    00efc47c-675a-45a7-b1fc-fc38c54360cc-image.png
    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)
    66c7638e-382b-4e6b-9c8d-212555dc5016-image.png
    Open it and then you can see the full sequence with all desired information in the first line.
    eb84c758-1071-4b1f-b6a5-b00671fc37bf-image.png
    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.
    a9cd6677-db3c-46f9-b1da-5e724b057094-image.png
    0be5537f-c72d-4b5b-8ace-e5063c559391-image.png
    Then select Protein date bank database as reference
    3cc36e82-66f6-4c38-ba2c-243cf86efe66-image.png
    Then Click on the BLAST Icon
    f148ae45-31f7-4fb1-8b62-0134b52aee2e-image.png
    It might take some seconds
    b5e9fcd9-78ef-4cf6-9663-5803bf01e7be-image.png
    It will show a page like this
    d0988cdf-fdf5-445f-b27b-5b5e8675e3c3-image.png
    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
    dfe5277b-e72d-4d5b-9b25-625f6727dbcf-image.png
    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.
    8753e4c8-b3f3-416a-8833-7eaeec79107b-image.png
    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.
    5245c6ab-1997-4f06-a1f4-bc8bd5214886-image.png
    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.


  • Cyberian's Gold

    @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
    11c278ed-e4bc-4217-999d-3a415a59f237-image.png
    Open NCBI
    da54bdc9-515e-4a47-ac88-00186f9509cc-image.png
    Select Protein database from here
    aba43dd4-1739-478e-b3f8-1fcd1fa1ffea-image.png
    Enter the name of your candidate gene (a gene, which you want to work upon)
    00efc47c-675a-45a7-b1fc-fc38c54360cc-image.png
    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)
    66c7638e-382b-4e6b-9c8d-212555dc5016-image.png
    Open it and then you can see the full sequence with all desired information in the first line.
    eb84c758-1071-4b1f-b6a5-b00671fc37bf-image.png
    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.
    a9cd6677-db3c-46f9-b1da-5e724b057094-image.png
    0be5537f-c72d-4b5b-8ace-e5063c559391-image.png
    Then select Protein date bank database as reference
    3cc36e82-66f6-4c38-ba2c-243cf86efe66-image.png
    Then Click on the BLAST Icon
    f148ae45-31f7-4fb1-8b62-0134b52aee2e-image.png
    It might take some seconds
    b5e9fcd9-78ef-4cf6-9663-5803bf01e7be-image.png
    It will show a page like this
    d0988cdf-fdf5-445f-b27b-5b5e8675e3c3-image.png
    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
    dfe5277b-e72d-4d5b-9b25-625f6727dbcf-image.png
    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.
    8753e4c8-b3f3-416a-8833-7eaeec79107b-image.png
    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.
    5245c6ab-1997-4f06-a1f4-bc8bd5214886-image.png
    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.



    Recent Topics


  • 3
  • 1
  • 23
  • 1
  • 2
  • 3
  • 1
  • 3
|