BIMM-143 - Introduction to Bioinformatics - Preparing for the Final Exam

Aug 30, 2026

Uploaded by Connor

BIMM-143 prepares students for an open-book, open-notes 150-minute final exam with 35 questions and 80 total points. The assessment focuses on key bioinformatics capabilities across major topics including database querying across core resources, sequence and structure representations, alignment via dynamic programming and scoring matrices, and limits of homology detection with BLAST-family and HMM-based tools. Additional coverage includes using R for data import, exploratory visualization, reproducible scripting, clustering and PCA interpretation, and protein sequence–structure–function analysis with Bio3D and in silico docking for drug discovery.

LanguageEnglish

CategoryExam

FormatPDF

Pages7

Reading Time18 min

AccessFree to download

Preparing for the Final Exam

Exam format and rules

Lecture 1: Bioinformatics databases and data representation

Lecture 2: Sequence alignment and dynamic programming

Lecture 3: Scoring, homology detection, BLAST/PSI-BLAST/HMMER

Lecture 4: Using R for bioinformatics data import

Lecture 5: Exploratory data analysis and visualization

Lecture 6-9: Writing R functions, packages, clustering

Lecture 10: Git excluded from the exam

Lecture 11-12: Energy/dynamics paradigm, Bio3D, flexibility, docking

BIMM-143: INTRODUCTION TO BIOINFORMATICS [http://thegrantlab.org/bimm143](http://thegrantlab.org/bimm143) Preparing for the Final Exam Overview: The ﬁnal exam for BIMM-143 will be an open-book, open-notes 150-minute test consisting of 35 questions. Questions will be predominantly short answer (typically worth 2 points) with a number of more involved longer answer questions (typically worth 5 points) . The number of points for each question is indicated at the beginning of each question. There are 80 total points on offer. There will be no questions covering the material from lecture 10 (the git version control system) . However, major points from all other lecture material are examinable General exam guidance and test rules are provided at the end of this document. Major points from lecture 1. Understand the increasing necessity for computation in modern life sciences research. Be able to query, search, compare and contrast the data contained in major bioinformatics databases (GenBank, GENE, UniProt, PFAM, OMIM, PDB) and describe how these databases intersect. Be able to describe how nucleotide and protein sequence and structure data are represented (FASTA, FASTQ, GenBank, SAM/BAM, PDB) . Example question: What database should I visit to help determine the protein domains that my novel protein contains? Major points from lecture 2. Be able to describe how dynamic programming works for pairwise sequence alignment Appreciate the differences between global and local alignment along with their major application areas. BIMM-143 Page 1 of 7 Understand how aligning novel sequences with previously characterized genes or proteins provides important insights into their common attributes and evolutionary origins. Example question: Fill out the dynamic programming table for determining the optimum global alignment between sequences GATCG and GCTCA. Assume that a match is scored +3 and that mismatches and gaps are scored-1 each? Major points from lecture 3. Be able to calculate the alignment score between two nucleotide or protein sequences using a provided scoring matrix. Understand the limits of homology detection with tools such as BLAST Be able to perform PSI-BLAST, HMMER and protein structure based database searches and interpret the results in terms of the biological signiﬁcance of an e-value. Example question: What is the major heuristic shortcut that BLAST uses to speed up database searches? Major points from lecture 4. Understand why we use R for bioinformatics. Familiarity with R’s basic syntax. Be able to use R to read and parse tab and comma-separated (.csv) formatted ﬁles ready for subsequent analysis. Familiarity with major R data structures (vectors, matrices and data.frames) Example question: What is the base R function for importing a tab-separated-value (tsv) format ﬁle for further analysis in R? Major points from lecture 5. Appreciate the major elements of exploratory data analysis and why it is important to visualize data. BIMM-143 Page 2 of 7 Be conversant with data visualization best practices and understand how good visualizations optimize for the human visual system. Be able to generate informative graphical displays including scatterplots, histograms, bar graphs, boxplots, dendrograms and heatmaps and thereby gain exposure to the extensive graphical capabilities of R Example question: What is the R code to generate the following scatterplot including axis labels, point colors and lines? Major points from lecture 6. Understand the structure and syntax of R functions and how to view the code of any R function. Understand when you should be writing functions. Be able to follow a step by step process of going from a working code snippet to a more robust function. Example question: What are the major component parts of an R function? Major points from lecture 7. Be able to ﬁnd and install R packages from CRAN and bioconductor, Understa

FAQs

What are the exam format and total scoring details for BIMM-143?

The final exam is an open-book, open-notes 150-minute test with 35 questions and 80 total points.

Which lecture material is explicitly excluded from the BIMM-143 final exam?

Material from lecture 10 (the git version control system) will not be covered on the exam.

What R-related skills are expected in BIMM-143?

Students should be able to import and parse tsv/csv files, understand core data structures, apply exploratory data analysis and visualization, and use R functions and packages to support reproducible workflows.

Aug 30, 2026

Uploaded by Connor