Topic outline

  • Welcome Note !

      Dear Students,

      Welcome to the 2022 Fall Semester!

      Welcome back, Students. I can’t wait to see all your smiling faces again! I am here to support you every step of the way.

      I encourage you to make the most of your time here.

      Remember to make it a great year. I will see you soon.


    Zerin Nasrin Tumpa
    Lecturer, Dept. of CSE
    Daffodil International University
    Email: zerintumpa.cse@diu.edu.bd
    Phone: +8801835531409



    • Calender : Click here

    • Instructions/Guideline for the course:

      • All the students of section O3, O4 for this course have to enroll in Moodle.
      • Students can find all the course materials from Moodle.
      • All the students have to submit the soft copy of their "Assignment" in Moodle under assignment section created here and for this they will be graded here.
      • One discussion or feedback forum is created under each of the lecture Students have to give their feedback on these forum and marks will be given for their feedback
      • Any announcement regarding the class will be posted on Moodle. So they have to keep themselves always active on Moodle.
      • All the quizzes and presentation will be conducted here and will be announced prior.
      •  The question pattern and the syllabus for the quizzes, midterm and final exam will be given prior that exam (quizzes, midterm and final).

    • Course Rationale:

       Bio-Informatics has been the most used methods of incorporating intelligence of biological world to computer science. It is therefore necessary to develop a good understanding of their operation and how they can be used as building blocks for computerized application of biology. This course explores the inner workings of a biological world from the programmer’s perspective by implementing different algorithms of Computer Science.


    • Course Objectives

      • To gather knowledge about biological world and relation with Computer Science and Engineering 
      • To analyze some existing methods and algorithms for specific biological problems
      • To grow the research interest in the field of Bioinformatics
      • To know the scope of bioinformatics research area and motivate them for research work.

    • Course Outcomes (CO’s): 

      • CO1: Understand the basics of Bioinformatics such as molecular and cellular biology, DNA sequencing, Gene duplication, Paralog, Ortholog, Homolog, Selectivity, Sensitivity, Phylogenetic Tree. 
      • CO2: Analyze algorithms for various existing methods for specific topic such as Global and Local Alignment, FASTA, HMM, Parsimony, Distance Approach, Maximum Likelihood Estimation. 
      • CO3: Ability to design and evaluate algorithms for specific biological problems. 


    • Assessment Plan File

      Grading Scheme

                         Attendance          :7%

                           Class Test          :15%

                       Presentation          :8%

                         Assignment         :5%

      Mid Term Examination        :25%

               Final Examination      :40%

                                Total            : 100%


    • Text Book Folder

      Book-1                                                 Book-2           

    • Reference Book Folder

      Book-1                                                            Book-2  

    • Course Outline:  Click Here

    • ***Telegram Group Link [Section O-3]

      Restricted Not available unless: You belong to (Missing group)

    • ***Telegram Group Link [Section O-4]

      Restricted Not available unless: You belong to (Missing group)

  • Week-1: Introduction to Bioinformatics


    • Topics to Discussion
      1.  Basics of Bioinformatics- Cell, Gene, Genome
      2.  Scope of Bioinformatics

      Expected Learning Outcome

      1.  Able to understand the relation between computer Scientists with Biologists
      2.  Able to grow research interest in this field

    • Lecture Content

    • Additional Materials

      • ▹Cell Structure -

    • Watch the recording of 1st class 

      Restricted Not available unless: You belong to (Missing group)

    • ***Self Test***

      1. Write 5 differences between DNA and RNA.


    • Submit the feedback form

    • Discussion Forum
      View Make forum posts: 1

  • Week-2: Molecular and Cellular Biology

    • Topics to Discussion
      1.  Basics of Molecular Biology-DNA, RNA
      2.  Structure of DNA and RNA, DNA Replication 
      3.  Cell Division- Mitosis and Meiosis

      Expected Learning Outcome

      1.  Able to understand the structural and functional difference between DNA and RNA
      2.  Able to know how the cell division is occurred in a cell and DNA Replication

    • Lecture Content

    • Additional Materials

      ▹DNA Structure -
      ▹DNA Replication - 

    • 1. Live class with section O-4

      Restricted Not available unless: You belong to (Missing group)

    • 2. Live class with section O3

      Restricted Not available unless: You belong to (Missing group)


    • ***self test***
      Annotate the deoxyribose sugar, nitrogen bases, hydrogen bond and phosphate in the following figure.


    • Submit the feedback form

  • Week-3: Gene Structure and Splicing

    • Topics to Discussion
      1.  Gene Structure, Gene regulation and Splicing  
      2.  DNA --> RNA --> Protein

      Expected Learning Outcome

      1.  Able to understand of Functional and non-functional parts of Gene 
      2.  Realize the process of Protein synthesis through translation and transcription process

    • Lecture Content

    • Additional Materials


      ▹Central Dogma - 


    • Submit the feedback form

    • Assignment 1
      Opened: Sunday, 4 September 2022, 12:00 AM
      Due: Sunday, 11 September 2022, 7:00 PM
      View Make a submission
    • Demo Quiz
      Opened: Monday, 5 September 2022, 10:00 AM
      Closed: Thursday, 8 September 2022, 10:10 AM
      View

  • Week-4: DNA Sequencing

    • Topics to Discussion
      1.  Basic terminologies to perform DNA sequencing
      2.  DNA Sequencing Process- Sanger Method
      3. Different G      enerations of Sequencing

      Expected Learning Outcome

      1.  Able to understand the DNA Sequencing Process
      2.  How Gnome Sequencing is performed in different generations

    • Lecture Content

    • Additional Material

      ▹Sanger Sequencing -

    • Discussion Forum
      View Post replies: 1

    • ***Live Class with section O4

      Restricted Not available unless: You belong to (Missing group)

    • Submit the feedback form

  • Week-5: Sequence Alignment

  • Week-6: Multiple Sequence Alignment

  • Quiz

    • Quiz-1 Section O3
      Opened: Tuesday, 13 September 2022, 10:30 AM
      Closed: Tuesday, 13 September 2022, 12:30 PM
      Restricted Not available unless: You belong to (Missing group)
    • Quiz-1 Section O4
      Opened: Tuesday, 13 September 2022, 10:30 AM
      Closed: Tuesday, 13 September 2022, 12:30 PM
      Restricted Not available unless: You belong to (Missing group)
    • Quiz-2 section O-3
      Opened: Saturday, 17 September 2022, 5:15 PM
      Closed: Saturday, 17 September 2022, 7:15 PM
      Restricted Not available unless: You belong to (Missing group)
    • Quiz-2 section O-4
      Opened: Saturday, 17 September 2022, 5:15 PM
      Closed: Saturday, 17 September 2022, 7:15 PM
      Restricted Not available unless: You belong to (Missing group)
    • Assignment-01
      Opened: Saturday, 15 October 2022, 12:00 AM
      Due: Friday, 28 October 2022, 12:00 AM
      Make a submission
    • Quiz-3[O-3]
      Opened: Friday, 9 December 2022, 7:15 PM
      Closed: Friday, 9 December 2022, 7:42 PM


      Question Type: MCQ

      Number of maximum attempt: 1


    • Quiz-3[O-4]
      Opened: Wednesday, 2 November 2022, 11:00 AM
      Closed: Wednesday, 2 November 2022, 11:30 AM
      Restricted Not available unless: You belong to (Missing group)

      Syllabus: Lecture 7,8,9,10

      Date: 15 August 2020

      Time: 11AM-11:30AM

      Question Type: MCQ

      Number of maximum attempt: 1


  • Week-7: Mid-Term Exam

    • Mid Examination Summer 2020 [CSE235] Assignment
      Opened: Monday, 26 September 2022, 2:10 PM
      Due: Monday, 26 September 2022, 6:00 PM
      View Make a submission

      Exam duration: 4 hrs [2:00PM - 6:00PM]

      Full Marks: 25

      Read the guidelines for penalty details and others.

      Be aware of plagiarism. It will be checked by the Turnitin Plagiarism Plugin.  

      Best of luck!!



  • Presentation

    • Topics of discussion:

       Prepare .ppt Slide to Present Your Selected Topic


      Upload Your Video Presentation

      1. Prepare a ppt with a maximum of 10 slides.
      2. Add voice narration and send the recorded ppt with voice narration 
      3. Presentation Duration: 3-4 Minutes (Max).
      4.Presentation Topic: Tell about yourself. You may include funny facts about you, or about your hobby, or dream job, or all of these! 

      5. Click here to Submit

      6. The name of your presentation video file must follow the naming convention, "CourseCode_Section_ID". For example, CSE123_O1_181-15-1234

      7. Deadline : 6/8/2020



  • Week-8: Gene Duplication and Read Mapping

    • Topics to Discussion

      1.      Different types of mutations
      2.      Gene Duplication- Homolog, Ortholog, Paralog and Speciation
      3.      Read Mapping- Keyword tree, suffix tree, suffix array, Burrows Wheeler Transform

       Expected Learning Outcome

      1.      Able to know different types of mutations
      2.      Analyze and differentiate clearly ablout Homolog, Paralog, Ortholog and Speciation
      3.      Able to understand suffix tree, suffix array, Burrows wheeler transform

    • Lecture Content 

    • **Self Test


    • ***Live class with section O4 [18/7/2020]

      Restricted Not available unless: You belong to (Missing group)

    • ***Live class with section O3 [19/7/2020]

      Restricted Not available unless: You belong to (Missing group)

    • ***Live class with section O4 [21/7/2020]

      Restricted Not available unless: You belong to (Missing group)

    • ***Live class with section O3 [21/7/2020]

      Restricted Not available unless: You belong to (Missing group)

    • Submit the feedback form

  • Week-9: Database Searching

  • Week-10: HMM- Forward Algorithm

    • Topics to Discussion
      1.  Markov Chain Model, Notation
      2.  Probability of a Sequence for a Given Markov Chain Model
      3.  CpG Island
      4.  Hidden Markov Model- Forward Algorithm

      Expected Learning Outcome

      1.  Able to clear understand about Markov Chain Model, CpG Island
      2.  Able to implement Forward Algorithm using HMM

    • Lecture Content

    • Submit the feedback form

  • Week 11: HMM-Viterbi Algorithm

  • Week-12: Maximum Likelihood Estimation

  • Week-14: Final Examination

    • Syllabus:

      All topics from week-8 to week-12.

    • ***Please read the Open Book Final Exam Guidelines before participating the exam.

      ***You have to submit your answer scripts both in BLC and google form.
      ***Submit your answer script by this google form.

      ***If for any technical issue, you can not submit in google form, submit in BLC. Then when the technical issue is solved, submit in google form. Same case for BLC. No need to mail me for this.
      ***You do not need to mail the answer script. Submit in BLC and google form.


    • Final Exam Assignment
      Opened: Wednesday, 9 November 2022, 9:00 AM
      Due: Wednesday, 9 November 2022, 1:00 PM
      View Make a submission

      **Time: 9:00AM to 1:00PM

      **Make sure about the naming convention of your file.

      **No need to mail the exam script. Just submit in BLC and google form.


    • Final Assignment
      Opened: Monday, 12 December 2022, 12:00 AM
      Due: Tuesday, 20 December 2022, 12:00 AM