Examples

• 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