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HMM Project Pipeline

1 Retrieve Sequences

Files stored within Sequence Retrieval

2 Format Sequences

Files stored within Format Sequences

3 Divide Across Ten Fold

Files stored within Ten Fold

4 Align the 90percent sequences across each fold

Using the Command (clustalo executable included in repo):

SGE_Batch -c 'clustalo -i 90percent.fasta --guidetree-out=90percent.dnd --threads=30 --outfile=90percentalign -v' -r outLog

5 Color Tree, Propagate, etc.

Files stored within Propagate

6 Get a Master Results table

Combine all the results from the 10 directories.

  • Remove the headers

7 Split Master Results table based on KO

Files stored within Split

8 Remove the unannotated Sequences

Files stored within Remove Unannotated

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