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Fig. 4 | BMC Bioinformatics

Fig. 4

From: Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0

Fig. 4

a The query form of the EdiFacts database module. Users may select to search for species, organelle, editing factor name, gene, editing site, factor-specific features such as length of the PPR arrays or carboxyterminal domains or authors of the corresponding publications to query the database. Boolean (AND/OR) logic can be adjusted where appropriate. The example shown reflects the search for characterized editing factors affecting the Physcomitrella patens ccmFC gene. b The EdiFacts output for the query shown under A retrieves Physcomitrella editing factors PPR_65 and PPR_71. Direct links to the respective protein sequences and literature reports are provided. c The PREPACT commons output highlights editing events ccmFCeU103PS and ccmFCeU122SF in Physcomitrella patens by italics and underlining to indicate that editing factors have been characterized for these RNA editing events. Clicking on these sites links to the entries for PPR_65 and PPR_71 in the EdiFacts database as shown under B. The ccmF homologues are notoriously complex owing to independent disruptions into separate ORFs and alternative gene names, which is accounted for by synonymizing in the PREPACT references (see output header). Shown is the example for the Physcomitrella patens ccmFC gene as a query run against the 10 selected references given in the header in BLASTX mode (see Fig. 1). The new “or reference site” option allows to include documented rare, unexpected or “orphan” editing events – in this example in Amborella, Liriodendron, Nicotiana and Arabidopsis – although below the overall default threshold level of 70% for display

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