D radiodurans
synteny analyser

Replicons synteny analyzer

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Blastp results from D radiodurans self-match (A2G07/DR/atig/btig genes with blastp, P max value=1e-²⁰) where used to link every replicon (or contig) to others according to their respective genes similarity.
This page displays the complete replicon list, ordered by replicon link and genes/link number.
List display can be controled by modifying "linking thresholds" min/max parameters,
such as number of links of each replicons, number of genes in each link,
as well as choosing min/max thresholds (bitscore & P value) for each gene match
Selecting a replicon unrolls the complete links for the given item with the number of matching genes for each link

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

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

Finding linked replicons paths becomes available when a replicon 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 replicons 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