They require a large amount of catalase activity to reduce high concentration of reactive oxygen species involved in the wood decay [44]. Comparative and evolutionary analysis, such as the above-mentioned

example, can be done on other families of peroxidases as well. Utility and discussion The web interface of fPoxDB provides an easy-to-use genomics environment. Intuitive menu structure and browsing system enable users to easily explore fPoxDB. fPoxDB provides browsing functions, gene distribution table and charts, pre-computed results of eight bioinformatics tools including InterPro scan [21], SignalP 3.0 [45], SecretomeP 1.0f [46], TMHMM 2.0c [47], PHA-848125 in vitro TargetP 1.1b [48], PSortII [49], ChloroP 1.1 [50], and predictNLS [51], as well as job submission forms for BLAST [41], HMMER [31], BLASTMatrix [32], and ClustalW [42] (Figure 3). In addition, the sequence profiles which were used in prediction of putative peroxidase genes can be downloaded, enabling large scale analysis such as whole proteome search Bortezomib on local computers. Figure 3 Web interface and functionalities. A) Web interface of fPoxDB displays well organized graphical charts for better recognition of the distribution of the genes. B) Tools including similarity search (BLAST [41], HMMER [31] and BLASTMatrix [32]) and multiple sequence alignment (ClustalW [42]) are provided

via the Favorite Browser. C) Protein domain analysis and TMH analysis can be also done with the sequences collected in Favorites. D) Users’ sequence collection can be further analysed by the tools available at the CFGP 2.0 [32] and other sister databases [39, 52–54]. Dynein “Browse by Species” displays species name, find more taxonomy, and the number of predicted peroxidase genes/gene families. For each species, the detail page shows the number of predicted

genes for each gene family as a graphical chart and table to present an overview on the peroxidase composition in a genome. The hierarchy implemented in the browser is easy to follow, so that users can readily retrieve data. “Browse by Species” also provides the taxonomically ordered summary table for every peroxidase family where kingdom-level and subphylum-level distribution are available. A summary of the whole database that describes the number of predicted genes against each genome can be downloaded as .csv format. This could provide the possibility to study gene family expansion or contraction across a number of genomes. “Browse by Classes” lists the peroxidase gene families and the number of genes and genomes corresponding to each gene family. Distribution of genes for each gene family is depicted in a box plot in order to show subphylum-level of taxonomic distribution at a glance. These distribution summaries could be used for searching peroxidase families which are limited to a certain range of taxonomy, such as LiP and MnP.