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Finds PfEMP1 DBL-alpha tags within larger sequence regions

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Octocat-spinner-32 bin
Octocat-spinner-32 data
Octocat-spinner-32 lib
Octocat-spinner-32 spec
Octocat-spinner-32 .document
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Octocat-spinner-32 .rspec
Octocat-spinner-32 Gemfile
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Octocat-spinner-32 LICENSE.txt
Octocat-spinner-32 README.md
Octocat-spinner-32 Rakefile
Octocat-spinner-32 VERSION
Octocat-spinner-32 bio-dbla-finder.gemspec
README.md

Introduction

DBL-alpha tags are short regions of the var gene and found within the first DBL domain of the molecule. The tags are characterised by degenerate motifs at the N and C-terminus. this tool extracts DBLa tag regions from larger sequences or contigs.

Processing a fastq file

  require 'bio-dbla-finder'
  file_path =  "path_to/myfasta_file.fastq"

  #create a finder class in this case named robot
  robot = Finder.new(file_path)

  #call the find_tags method to list the tags to the stderr
  robot.find_tags

Copyright and Licensing

Copyright (c) 2011 George Githinji. See LICENSE.txt for further details.

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