BSC 2435 - Introduction to Bioinformatics

College of Natural Sciences

Credit(s): 3
Contact Hours: 47
Effective Term Fall 2022 (610)

Requisites

(Prerequisite BSC 2010 with a minimum grade of C and
(Prerequisite BSC 2010L with a minimum grade of C or
Prerequisite BSC 2010CH with a minimum grade of C)
) and
(Pre- or Co-requisite BSC 2420 with a minimum grade of C and
Pre- or Co-requisite PCB 2061C with a minimum grade of C)

Course Description

Students will gain hands on experience in performing bioinformatics analysis using both nucleic acids and protein sequences. Use of open source software and publicly available databases such as NCBI will be demonstrated and conceptual understanding of associated algorithms and statistics will be applied to resulting data analysis. Specific topics to be covered include file formatting and management; retrieval, submission, and alignment of sequences using the most current tools; gene expression; phylogenetics; and primary literature searches. This is not a programming course. This course is designed to be taught in a blended or on-line modality.

Learning Outcomes and Objectives

  1. The student will analyze the basic molecular biology and chemistry of nucleic acids and proteins as relevant to bioinformatics applications by:
    1. explaining the processes of DNA replication, transcription and mRNA translation.
    2. illustrating the chemical structure of nucleic acids and proteins.
    3. identifying functional components of gene and genome structure.
    4. comparing the four levels of protein structure.
    5. applying knowledge of chemical bonds to sequence and functional analysis.
  2. The student will evaluate the differences and appropriate uses of laboratory based in vitro and in vivo techniques in relation to in silico based technology by:
    1. solving restriction mapping problems.
    2. designing probes for application in knockdown technology, gene expression detection, and primer design compatible with current PCR technology.
    3. explaining the process of sequencing using Sanger and Next Generation Sequencing (NGS) technologies.
    4. performing software assisted vector engineering and relevant recombinant technology to generate molecular construct, clones and clone libraries.
  3. The student will conduct database searches by:
    1. retrieving current primary literature articles using PubMed, PubChem and other relevant literature search engines.
    2. performing NCBI BLAST searches.
    3. using database appropriate commands and file formats to retrieve, compare and when possible contribute sequences to public genome databases.
    4. evaluating the results of sequence searches through Entrez, GenBank and other international and species-specific genomic search engines.
  4. The student will characterize and compare nucleic acids sequences by:
    1. explaining the concepts behind sequence alignment algorithms.
    2. assessing sequence alignment quality by deciphering software-specific scoring and statistical significance.
    3. using CLUSTALW2, Mega and other currently relevant software programs to compare two or more sequences.
    4. identifying molecular, structural and functional hallmarks including but not limited to intron and exon boundaries, genetic regulatory elements and patterns of epigenetic modifications.
    5. performing standard sequence manipulations such as six frame translations and open reading frame identification.
  5. The student will characterize and compare proteins by:
    1. using CLUSTALW2, Mega and other currently relevant software programs to compare two or more sequences.
    2. predicting protein biochemical properties using primary amino acid sequence.
    3. determining potential protein structure using comparative and predictive modeling.
    4. assessing post translational modifications based on sequence.
  6. The student will evaluate genetic and genomic similarities by:
    1. performing molecular phylogenetics.
    2. discussing differences in phylogenetic tree generation using distance matrix methods including but not limited to neighbor-joining and transformed distances.
    3. reporting confidence levels associated with comparative analysis of genes and genomes.
    4. organizing and managing large data files.
    5. generating meaningful figures representing genome wide analysis and systematics.
  7. The student will investigate gene expression by:
    1. defining the genetic code as it pertains to mRNAs.
    2. predicting promoter elements and splicing signals.
    3. performing searches using unknown sequences queried against cDNA and EST databases.
    4. using current transcriptomics data (i.e. tiling arrays) and relevant software to evaluate tissue-specific expression.

Criteria Performance Standard

Upon successful completion of the course the student will, with a minimum of 70% accuracy, demonstrate mastery of each of the above stated objectives through classroom measures developed by individual course instructors.

History of Changes

C&I Approval: 11/21/2014, BOT Approval: 02/17/2015, Effective Term: Fall 2015 (505). C&I Approval: 02/09/2018, BOT Approval: 04/17/2018, Effective Term: Fall 2018 (550). C&I Approval: , BOT Approval: , Effective Term: Spring 2021 (585).
C&I Approval: , BOT Approval: , Effective Term: Fall 2022 (610)

Related Programs

  1. Biotechnology Laboratory Technology (BIOT-AS) (640) (Active)
  2. Biotechnology Laboratory Technology (BIOT-AS) (635) (Draft)
  3. Laboratory Specialist (LAB-ATC) (670) (Active)