CRS alignments

para = window.location.href.match(/(?<=candidate=)(.*?)[^&]+/)
sv = {
  if ( para !== null ) {
    if ( motifs_list.includes(para[0]) ) {
      return para[0]
    }
  }
  return motifs_list[0] 
}

infoHelper = function(x, lab, txt) {
  // The element to show
  let res = html`${lab} <span class='myInfo' id='${x}'>ⓘ</span>`
  // Add tippy tooltip
  // Iusse: add with delay, otherwise the span was not yet displayed
  setTimeout(function() {
    tippy('#' + x, {
      content: txt 
    })
  }, 500)
  return(res)
}

// Choose a single motif
viewof sel = Inputs.select(
  motifs_list,
  {
    label: 'Alignment for',
    value: sv
  }
)

html`<a href="https://rth.dk/resources/crs/cyanobacteria/candidate.html?candidate=${sel}">View CRS details</a>`

Post-processed alignment

html`Download alignment as <a href="https://rth.dk/resources/crs/cyanobacteria/data/motifs/${sel}.sto">Stockholm</a> | <a href="https://rth.dk/resources/crs/cyanobacteria/data/motifs-fasta/${sel}.fasta">Fasta</a> | <a
href="https://rth.dk/resources/crs/cyanobacteria/data/cm/${sel}.cm">Covariance model</a> | <a href="https://rth.dk/resources/crs/cyanobacteria/data/jalview/${sel}.svg">Figure</a>`

html`<center><img src="https://rth.dk/resources/crs/cyanobacteria/data/jalview/${sel}.svg" class = 'jalview'/></center>`

Filtered alignment

• all sequences were removed that have a nucleotide in an alignment column with more than 95% of gaps
• sort sequences based on their Hamming distance to the most central sequence (based on total Hamming distance)

html`Download alignment as <a href="https://rth.dk/resources/crs/cyanobacteria/data/motifs-gapfree/${sel}.sto">Stockholm</a> | <a href="https://rth.dk/resources/crs/cyanobacteria/data/motifs-fasta-gapfree/${sel}.fasta">Fasta</a> | <a
href="https://rth.dk/resources/crs/cyanobacteria/data/jalview-gapfree/${sel}.svg">Figure</a>`

html`<center><img src="https://rth.dk/resources/crs/cyanobacteria/data/jalview-gapfree/${sel}.svg" class = 'jalview'/></center>`

Visualization made with Jalview.