Thus, a 100%% of similarity was identified with both, the pairwise alignment algorithm of Smith-Waterman implemented on the EMBOSS Website [48] and the CLICK software [49].
The presence or absence of the C-terminal acidic region in FlbE orthologs was determined by using the Grantham method [77] as implemented on the ExPASy website (http://www.expasy.org/tools/protscale.html) [78] using a window of 15 residues.
The functional clustering was performed using the method implemented on the DAVID website http://david.abcc.ncifcrf.gov/.abcc.ncifcrf.gov/
All programs used to detect selection, including SLAC, MEME and BGM, were implemented on the DataMonkey website [ 39].
Another important feature of the networks, as implemented on the NVC website, is that they are dynamic: they can be modified to represent specific species and/or tissue contexts by the application of appropriate boundaries and can be updated as new knowledge becomes available.
In phase I, the interRAI PC is adapted for use in Belgium and implemented on the BelRAI-website and a practical training is developed.
The top 9 homologs of Spl11 (Os12g38210) in the rice genome were identified by blasting the Spl11 CDS against "Genes in TIGR Rice Pseudomolecules-CDS" using WU-BLAST 2.0 implemented on the TIGR Rice Genome Annotation website (http://www.tigr.org/tdb/e2k1/osa1/ [40]. Most of them are annotated as "spotted leaf protein 11, putative" (Table S3).
Final models were verified with the program MolProbity (Chen et al., 2010 ) and crystal contacts analyzed using the PISA algorithm implemented on the Protein Data Bank Europe website (Krissinel and Henrick, 2007 ).
The new scoring is implemented on the Protein Prospector public website at: http://prospector.ucsf.edu.
