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sborstein / AnnotationBustR

AnnotationBustR
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Issues with Complement Strand Sequence #6

Closed sborstein closed 8 years ago

sborstein commented 8 years ago

Complement strands, do they need to be flipped and reversed/coded? Example: [http://www.ncbi.nlm.nih.gov/nuccore/KU301747.1]

Look at ND6. That and a few tRNA genes are on the light strand, which is complementary to the heavy strand. If you look for the start codon, it is the last three nucleotides.

sborstein commented 8 years ago

Possible solution:

  1. gsub .. for : which R can read as an interval
  2. paste in a "-" in front of all parts within the complement(*), and remove complement. This way we know which need to be converted to reverse complements.
  3. Make search for the join, we no longer need a complement part.
sborstein commented 8 years ago

Solved using a different function without finding sequence positions. Can now perform complex extractions.