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Sequence Similarity: A Quick Introduction to Bioconductor

Author(s): Derek Edward Sollberger

Princeton University

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Summary:
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.

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

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

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

Keywords

  1. bioinformatics
  2. sequencing
  3. NIBLSE
  4. multiple sequence alignment
  5. sequence similarity
  6. BLOSUM scoring matrix
  7. Bioconductor

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  4. NIBLSE Core Competencies
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Contents:
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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.’’

 

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. CourseSource. https://doi.org/10.24918/cs.2019.5

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