This function allows to load coupling scores sorted by importance to display contacts on the MSA.
The 1bkr:A coupling scores can be downloaded here.
Prerequisite: the file format is a comma-separated file (.csv), such as what gets outputted by evcouplings.org when selecting the "Raw Evolutionary
(EC) table" option.
Once loaded, the MSA view tab will display colored ellipses.
The same colored ellipse on two different residues represents a contact between the pair.
A maximum of 20 ellipses will be displayed.
Load the couplings already sorted by strength. The residues start from the position zero.
File format is tab-separated text file with two columns: the position numbers of the coupled residues
contacts position B)
Not all positions have to be present and only few will be displayed.
Load custom sequence annotation to be shown along the alignment as sortable column.
File format is tab-separated text file with two columns: sequence name as in your multiple sequence
(MYG_HUMAN/1-154), annotation (numerical or text).
The example for 1bkr:A can be downloaded here.
Not all sequence names have to be present - can provide as few as one to move it up when sorted.
Position of reference sequence is maintained in sorted msa.
ident1% = fraction of reference sequence identical to second sequence (gaps not
ident2% = fraction of second sequence identical to reference sequence (gaps not
gap & conservation bar chart
Color columns with conservation higher than:
Currently showing sequences:
Hide sequences with gaps higher than
Hide sequences with identity1 lower than
Sequence space view of sequences from the multiple sequence
Dimensionality reduction is carried out using the UMAP algorithm (arXiv e-print) as implemented using umap-js (github).
To visualize sequence classes, please upload an annotation.