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Bioinformatics: the Power of Computers in Biology – a Practical Guide

Author(s): Daniel Barker1, Heleen Plaisier2, Stevie Anne Bain1, Teresa Attwood

1. The University of Edinburgh, Edinburgh, UK 2. Royal Botanic Garden, Edinburgh, UK

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Summary:
This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces simple bioinformatics approaches for database searching and sequence analysis.

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

Version 1.0 - published on 03 Dec 2020 doi:10.25334/QBB5-7G72 - cite this

Keywords

  1. NIBLSE
  2. GOBLET

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  3. NIBLSE Core Competencies
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Description


This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces simple bioinformatics approaches for database searching and sequence analysis. A ‘mystery’ gene is used as an exemplar: we first characterise the gene, then use it to explore the impact of gene loss in humans. Analyses are run both online and at the command line, the latter using Raspberry Pi computers running the 4273π variant of Linux (4273pi.org).

Specifically, this Guide introduces a popular Web-based tool for searching biological sequence databases, and shows how similar functionality can be achieved using the Linux command line. On reading the Guide and completing the exercises, users will be able to:

  •     search biological sequence databases using the online program BLAST, and navigate GenPept sequence records;
  •     execute some basic Linux commands to perform a set of simple file-manipulation tasks;
  •     perform BLAST searches via the Linux command line; and
  •     evaluate the biological implications of search results, with reference to mutations and function.

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