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The Human Genome and Personalized Medicine

  • August 15, 2020August 19, 2020
Developed by Dr. Anya Goodman (California Polytechnic State University) and Dr. James Youngblom (California State University Stanislaus), this computer laboratory is designed to introduce students to the analysis of DNA sequences and to the effects of bioinformatics on access to health information by scientists, doctors, and the general public.

Plant Genes Annotation and Analysis

  • August 15, 2020August 19, 2020

This is a series of three 3-hour exercises that guide students on the DNA Subway, an online workspace that integrates tools for genomic analysis in a student and educator-friendly environment. Exercise 1 was developed by Dr. Judy Brusslan (California State University, Long Beach). The Exercise I and II PowerPoints and Exercise II were developed by Dr. James Youngblom (California State University Stanislaus). The “Prospecting for Green Revolution Genes” presentation and Exercise III were developed by Dr. Nicholas Ewing (California State University, Sacramento) based on materials initially developed by members of the iPlant Collaborative.

Finding Genes in a New Fly Genome

  • August 15, 2020August 19, 2020

This exercise was developed by Dr. Anya Goodman (California Polytechnic State University) and Dr. James Youngblom (California State University, Stanislaus). This exercise engages students in annotating genomic DNA from less famous species of Drosophila while teaching basic bioinformatics skills.

Genomic Annotation Lab Exercise

  • August 15, 2020August 19, 2020

Dr. Marian Kaehler (Luther College), in collaboration with Jacob Jibb, has written an annotation lab. This lab will ask students to annotate a gene from the D. erecta genome.

Bioinformatics Tools Tutorial Project – KRas

  • August 15, 2020August 19, 2020

This lab is an updated, stand-alone version of the bioinformatics exercise originally developed for Bio 3055 at Washington University. This exercise introduces students to the genetic basis of disease using the KRas protein.

Introduction to BLAST using Human Leptin

  • August 15, 2020January 2, 2022

Dr. Justin R. DiAngelo (Penn State Berks) and Dr. Alexis Nagengast (Widener University) have developed an exercise that introduces students to the basic functionality of the NCBI web site and NCBI BLAST. Students will use NCBI BLAST to identify the putative orthologs of the human Leptin gene in other species.

Using BLAST and ExPASy for Genetic and Protein Analysis of H1N1 Variability

  • August 15, 2020August 19, 2020

Ms. Julie Ertmann (University City High School, MO) has designed a standalone activity using BLAST for AP or second year high school biology students. This exercise uses BLAST and ExPASy for genetic and protein analysis of H1N1 variability, including mutations that confer resistance to antiviral medications. Development of this exercise was supported by an NSF Mathematics and Science Partnership grant #06344780, to B Schaal, Washington University in St. Louis. If you have questions about this activity, please email the author at: jertmann@ucityschools.org.

Investigating a Mutation in HIV-1

  • August 15, 2020August 19, 2020

Students use the HIV Problem Space on the BioQuest BEDROCK Website to investigate whether a specific HIV mutation can be correlated with a decline in immune system function. In order to perform this analysis, students must generate and analyze multiple sequence alignments of HIV sequences generated from the ALIVE study.

Module TSS2: Using Sequence Alignment to Identify a TSS

  • August 15, 2020January 2, 2022

This module illustrates how pairwise (blastn) and multiple sequence alignments can be used in conjunction with RNA-Seq data and the Short Match functionality of the UCSC Genome Browser to facilitate the TSS annotation of the Antp gene in D. eugracilis.

Basics of BLAST

  • August 15, 2020January 2, 2022

This PowerPoint presentation provides a brief introduction to the different kind of BLAST searches available.