QUBES - Resources

BLAST Exercises for Analyzing Cloning Results

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. These activities have modified Lesson 1: Introduction to Genome...

Keywords: Bioinformatics EducationBioinformatics and Genomics

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DNA Barcoding & Biodiversity databases

This resource pairs DNA barcoding databases with Biodiversity databases. Students collect their insect specimens in the field and use BLAST and BOLD to identify their species. They then use...

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Lesson I - Introduction to Genome Solver

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. Part I is the Introduction to the Genome Solver Project.

Keywords: Bioinformatics EducationBioinformatics and Genomics

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Understanding COVID-19 Biology to Design a Vaccine - Ethics supplement

The adaptation to Understanding COVID-19 Biology to Design a Vaccine entails two ethics supplements. The first supplement addresses the use of off-label drugs in the pandemic (or other situation)....

Keywords: bioethicsBLASTprotein structure modelingmolecular visualization and analysisethicsCOVID19PDB

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Lesson VI - The Community Science Project

Genome Solver's Community Science Project was developed as a way to use the skills taught in the previous lessons. We're asking members of the community to provide instances of potential phage...

Keywords: Bioinformatics EducationBioinformatics and Genomics

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Understanding COVID-19 Biology to Design a Vaccine

This multi-part case study introduces the reader to the SARS-CoV-2 virus, replication, and treatment. Additional worksheets introduce students to bioinformatics tools of 3-D protein visualization...

Keywords: BLASTprotein structure modelingmolecular visualization and analysisCOVID19PDB

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One species, two species, red species, lead species? Phylogenetics and species concepts with Plethodon salamanders

This lab introduces students to species concepts and basic computer-based tree-building methods using published nuclear and mitochondrial sequence data for Plethodon salamanders.

Keywords: phylogenetic analysisTree thinkingsalamanderAudience level - Advanced UG

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Sequence Similarity: Introducing Biological Databases to Community College Biology Students

This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.

Keywords: phylogeneticsbioinformaticssequencingFASTANCBINIBLSEalgorithmsincubatorsBLASTmultiple sequence alignmentsequence similarityBLOSUM scoring matrixneighbor-joining distance matrixCourseSourcephylogramZika virus

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Bioinformatics: Investigating Sequence Similarity - A Plant Biology Approach

This laboratory module is a modification of the original published on CourseSource with a focus on plant biology. In the final activity, students conduct a BLAST to compare histone protein...

Keywords: phylogeneticsbioinformaticssequencingFASTANCBIplant biologyNIBLSEalgorithmsincubatorsPlant and Fungal EvolutionBLASTmultiple sequence alignmentsequence similarityBLOSUM scoring matrixneighbor-joining distance matrixCourseSourcephylogram

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Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses

This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.

Keywords: phylogeneticsbioinformaticssequencingFASTANCBINIBLSEalgorithmsincubatorsBLASTmultiple sequence alignmentsequence similarityBLOSUM scoring matrixneighbor-joining distance matrixCourseSourcephylogramZika virus

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Hemoglobin bioinformatics

This is an introduction to bioinformatics using hemoglobin as an example. The worksheets introduce students to resources to explore the DNA, RNA and polypeptide linear structure with a brief...

Keywords: bioinformaticsHemoglobinBLASTsickle cell diseaseMolecular Case StudyClustal OmegaMolCaseNet

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Drugging SARS-CoV-2

This case study leads students through the process of proposing a drug for a novel protein. The Mpro protease of SARS-CoV-2 is explored in detail within the PDB. Aligns with first semester...

Keywords: viruscoronavirusPDBSARS-CoV-2proteasedrug design

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Evaluating the potential for immune escape: how likely is an antibody to protect against a specific SARS-CoV-2 variant?

Commercial antibodies to the SARS-CoV-2 spike protein have been successfully used to treat people with COVID-19. Unfortunately, as the SARS-CoV-2 virus evolves, new variants have appeared that can...

Keywords: course based undergraduate research experiencesBLASTmolecular modelingSARS-CoV-2antibodyNextstrainiCn3DSequence alignmentStructure alignment

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Evaluating the potential for immune escape: how likely is an antibody to protect against a specific SARS-CoV-2 variant?

Commercial antibodies to the SARS-CoV-2 spike protein have been successfully used to treat people with COVID-19. Unfortunately, as the SARS-CoV-2 virus evolves, new variants have appeared that can...

Keywords: course based undergraduate research experiencesBLASTmolecular modelingSARS-CoV-2antibodyNextstrainiCn3DSequence alignmentStructure alignment

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Inquiry-based hypothesis testing using phylogenetic trees in MEGA

A key learning objective in biology is applying bioinformatics tools to test a real-life question. These inquiry-based modules have students assemble and align data, and construct simple...

Keywords: phylogeneticsbioinformaticsFASTANCBIBLASTmultiple sequence alignmentsequence similarityCourseSourceZika virusMEGAalcohol metabolism

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Introductory Video and worksheets on Module 1 and 2 on "Sequence Similarity: An inquiry based and under the hood..."

The video walks the students to complete Module 1 and 2 on Sequence Similarly and Alignment adapted from Tapprich (2019) and Hudson Alpha that teaches these modules within the context of the...

Keywords: bioinformaticssequencingFASTANCBINIBLSEalgorithmsBLASTmultiple sequence alignmentsequence similarityBLOSUM scoring matrixCourseSource

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COVID-19: On the way to a vaccine

This multi-part case study introduces the reader to the SARS-CoV-2 virus origins, the molecular basis of the infection, the development and severity of symptoms, and treatment.

Keywords: BLASTprotein structure modelingmolecular visualization and analysisCOVID19PDB

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Developing a phylogram from computational resources.

This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.

Keywords: phylogeneticsbioinformaticssequencingFASTANCBINIBLSEalgorithmsBLASTmultiple sequence alignmentsequence similarityneighbor-joining distance matrixCourseSourcephylogrampercent identity matrix

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Open. Adaptable. Free.

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BLAST Exercises for Analyzing Cloning Results

DNA Barcoding & Biodiversity databases

Lesson I - Introduction to Genome Solver

Understanding COVID-19 Biology to Design a Vaccine - Ethics supplement

Lesson VI - The Community Science Project

Understanding COVID-19 Biology to Design a Vaccine

One species, two species, red species, lead species? Phylogenetics and species concepts with Plethodon salamanders

Sequence Similarity: Introducing Biological Databases to Community College Biology Students

Bioinformatics: Investigating Sequence Similarity - A Plant Biology Approach

Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses

Hemoglobin bioinformatics

Drugging SARS-CoV-2

Evaluating the potential for immune escape: how likely is an antibody to protect against a specific SARS-CoV-2 variant?

Evaluating the potential for immune escape: how likely is an antibody to protect against a specific SARS-CoV-2 variant?

Inquiry-based hypothesis testing using phylogenetic trees in MEGA

Introductory Video and worksheets on Module 1 and 2 on "Sequence Similarity: An inquiry based and under the hood..."

COVID-19: On the way to a vaccine

Developing a phylogram from computational resources.

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