pyhmmer 0.6.1
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ExamplesΒΆ

  • Build an HMM from an multiple sequence alignment
    • Loading the alignment
    • Building an HMM
    • Saving the resulting HMM
    • Applying the HMM to a sequence database
  • Analyse the active site of an enzymatic domain
    • Loading the HMM
    • Loading digitized sequences
    • Running a search pipeline
    • Rendering the alignments
    • Checking individual positions for catalytic activity
  • Fetch Marker Genes from a genome
    • Getting the cutoffs
    • Downloading the HMMs
    • Loading the sequences
    • Running the search pipeline
    • Filtering results
  • Run an iterative search to build a HMM for rhodopsins
    • Downloading sequence data
    • Running a simple search
    • Running a conservative iterative search
    • Running an iterative search with custom selection
    • Recording bitscore cutoffs
    • Saving the HMM

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© Copyright 2020-2022, Martin Larralde.
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