File Comparisons

vimdiff

• Vim is great! -- Diff is great too.
• Vim+Diff is a power tool for comparing up to 4 files simultaneously highlighting differences.
• Syntax/Highlight colours can be customized via the users ".vimrc" file (see highlight commands at bottom).
• Here vimdiff is used to compare the differences in Hamlet Q1 and Q2 (modern spelling editions) from Shakespeare Internet Editions.

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Aligning Sequences

Dynamic Time Warping (DTW)

• Guaranteed to find optimal alignment "path".
• dtw.py

~/DMU/msa_sandpit_2017.3.13> py dtw.py 0 3000 Ham_F1.html.txt Ham_Q1.html.txt "_"

	Q1	Q2
F1

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Multiple Sequence Alignment (MSA)

• Not guaranteed to find optimal alignments
• Heuristics
• Tools such as "muscle" and "clustalW"
  • Note that muscle uses an iterative (rather than progressive) method hence the results from muscle do not depend on the order that the sequences are given to it in the input Fasta File

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SEE Pipeline v0.1 08.03.17

• Try to map text into DNA or Protein alphabet

• pipeline.sh
• scrape.sh
• encode.py
• decode.hs
• toTree.py

• Tried DNA and Protein alphabets
• Problems -- split codons
  • Occasionally the alignment program might introduce a gap within a codon. This causes the output text to become nonsense (containing characters output as "\200" etc.) until a compensating corrupted codon fixes the alignment.

-- -X XX -- etc

This is more likely in "4 position DNA-type codon" than in "2 position Protein-type codon" experiments.