Evoldeep
Fosmids synteny analyser

Fosmids synteny analyzer

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Blastp results from EVOLDEEP libraries self-match (KM3/AD1000/SAT1000/SAG genes with blastp, P max value=1e-²⁰) where used to link every fosmid (or contig) to others according to their respective genes similarity.
This page displays the complete fosmids/contigs list, ordered by fosmid link and genes/link number.
List display can be controled by modifying "linking thresholds" min/max parameters,
such as number of links of each fosmids, number of genes in each link,
as well as choosing min/max thresholds (bitscore & P value) for each gene match
Selecting a fosmid unrolls the complete links for the given item with the number of matching genes for each link

Shared genes between 2 fosmids can be individually displayed as gene maps (push 'Link now' button) , or added to a linked list of fosmids ( check 'add link' checkbox) which appears in a floating window at left ('selected links')
Subsequently, chained fosmids can be displayed in gene maps ('Link' button in 'Selected links' float window)
Additionally, whenever a fosmid/contig is "Selected", a linked list of fosmids can be computed ('find linked fosmids paths' panel) using either most or less parsimonious paths

Toggle display of each fosmid links: click on a name (this can be done recursively) This opens up a panel with fosmids links and matching genes number This also selects the corresponding fosmid Display each matching gene within each link: pass pointer over matching genes number Immediately show link between 2 fosmids : push 'Link now' button Add a fosmid to the link list: check 'add link' checkbox. This disables recursive linking display for other non-selected fosmids of the same level Display multiply linked fosmids chain : push 'Link' in 'Selected links' float window

Finding linked fosmids paths becomes available when a fosmid is 'selected' Choose path discovery method (most/less parsimonious == max or min number of genes for each link) Set up min/max thresholds for path computations : Depth is for max number of fosmids in link chain Strength is for max/min number of genes in each link Path findings are computed in the scope of linking thresholds settings