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Sequence Similarity: A Quick Introduction to Bioconductor

By Derek Edward Sollberger

UC Merced School of Natural Sciences

Following the Sequence Similarity exercises by Kleinschmit, et al., this tutorial will guide students in using the Bioconductor suite of R packages to likewise compute sequence similarity.

Listed in Teaching Materials | resource by group Bring Bioinformatics to Your Biology Classroom

Version 1.0 - published on 04 Jun 2021 doi:10.25334/WTAG-3Y84 - cite this

Licensed under CC Attribution-NonCommercial-ShareAlike 4.0 International according to these terms

Adapted from: Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses v 5.0

sequence_sim.JPG

Description

In this bioinformatics adventure, we are going to continue to look amino acid sequences and compute similarity scores using the BLOSUM62 matrix, but we will take a glimpse at some of the tools that are available in the world of Bioconductor. This set of tasks are set after Exercise 3 in the Sequence Similarity materials

Bioconductor is a collection of R packages that has been built by several bioinformatics researchers to perform common calculations in their field. In their own words, ``Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, and an active user community.’’

 

Contents:

Quote

"If you want to build a ship, don’t drum up the men to gather wood, divide the work and give orders. Instead, teach them to yearn for the vast and endless sea." ---Antoine de Saint—Exupery

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Notes

  • Introduce students to the Bioconductor suite of R packages
  • Perform sequence similarity calculations

 

Reference

Kleinschmit, A., Brink, B., Roof, S., Goller, C., and Robertson, S.D.  2019. Sequence Similarity: An inquiry based and “under the hood” approach for incorporating molecular sequence alignment in introductory undergraduate biology courses. CourseSourcehttps://doi.org/10.24918/cs.2019.5

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