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The documentation is still in progress... but do not panic! If you have any question, we will be more than happy to answer it directly.
Panache uses a TSV file that extends BED format to allow the insertion of new information such as a presence absence matrix and functional categories. In practice, this is a 8 tabular column that stores start and stop positions of the chromosome blocks with presence/absence matrix (1/0) computed block similarity(optional), functional category (optional).
| Chrom | Start | Stop | Similar Blocks | Function | A | B | C |
|---|---|---|---|---|---|---|---|
| chr1 | 56 | 78 | chr2:74:96 | GO:0009819 | 0 | 0 | 1 |
| chr1 | 210 | 356 | - | - | 1 | 0 | 1 |
| chr2 | 500 | 4569 | chr4:120:133 | - | 1 | 1 | 1 |
Panache accepts a classical GFF3 format with gene structural annotation.
In the case you have a graph dataset at GFA, Graph can be linearized with BioGraph
TBD
Panache proposes a way to scan automatically a (pan)chromosome to find gaps of N (integer) consecutive block(s) that may be absent in a set of N individuals (ratio between 0 and 1). Parameters can be fine tuned and are calculated on the fly, updating the number of found areas. Left and right arrows enable users to jump from one area to another.
If a GFF file has been provided, dot (or square) appears in the interface and are clique to display gene structure and annotation in a popup.
Panache relies fully on javascript and once deployed on a server, it can be embedded easily in a existing application using an iframe.