BnIR, Brassica napus multi-omics database (information resource)

BnIR Brassica napus multi-omics information resource ————A multi-omics database with various tools for Brassica napus research and breeding

e.g. FLC or AT1G02970

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Multi Alignment Viewer

Gene ID/Fasta

?

e.g. example_1(gene list) or example_2(Fasta sequence)

Type Protein gDNA CDS

detected as input.
result(s) found in BnIR.

Multiple sequence alignment visualization & Analysis

msa view | image view | stats view |

Generate msa image using coloring :

residue width in pixels:
residue height in pixels:

Sequence gaps & ref.seq identity - amount of sequences with given fraction of gaps/identity (sorted by ranking)
Pairwise identity calculate
Pairwise identity 2D map	0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1

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.

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.

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.

ident1% = fraction of reference sequence identical to second sequence (gaps not counted)
ident2% = fraction of second sequence identical to reference sequence (gaps not counted)

Sequence order:
Coloring Scheme:

gap & conservation bar chart
sequence logo

Color columns with conservation higher than:

Currently showing sequences:

Filtering

Hide sequences with gaps higher than

Hide sequences with identity1 lower than

gaps/conservation

gaps%

ident1%

ident2%

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.