Multi Alignment Viewer
detected as input.
result(s) found in BnIR.
result(s) found in BnIR.
Multiple sequence alignment visualization & Analysis
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msa view
| image view |
stats view |
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| Sequence gaps & ref.seq identity - amount of sequences with given fraction of gaps/identity (sorted by ranking) | |
| Pairwise identity | |
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Pairwise identity 2D map
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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 Couplings (EC) table" option. An example: i,A_i,j,A_j,fn,cn,segment_i,segment_j,probability
49,V,69,M,0,0.050877,A,A,0.9985961719887426
57,S,65,D,0,0.045328,A,A,0.9918500685696678
52,R,73,V,0,0.042749,A,A,0.9835481279392891
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. |
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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 (position A contacts position B) Not all positions have to be present and only few will be displayed. |
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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 alignment (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. |
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gaps/conservation
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gaps%
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ident1%
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ident2%
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Sequence space view of sequences from the multiple sequence
alignment. 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. |
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