AUTOMATIC FUNCAT
The MIPS Functional Catalogue (FunCat) was developed in 1996 and used in the annotation of S.cerevisiae (8). It comprises a hierarchically structured classification system, which at first only contained categories describing yeast biology. Since then, it has been extended and used to annotate the following genomes: T.acidophilum, Bacillus subtilis 168, L.monocytogenes EGD, L.innocuaClip 11262, H.pylori KE26695, N.crassa, A.thaliana and H.sapiens. The most recent version of the FunCat (v. 2.0; 16) is organism independent and consists of 28 main categories, covering features such as metabolism and cellular transport, as well as some more recently introduced categories (e.g. development and organ localization). The main categories are assigned a unique two-digit number e.g. 01. metabolism, which appears as the first two digits of the FunCat number. The main categories are branched into more specific categories, with up to six levels of increasing specificity (e.g. 01.01.06.05.01.01 biosynthesis of homocysteine).
The PEDANT software calculates automatic FunCat numbers based on a gene product's similarity to proteins in the manually annotated protein FunCat database. Although assignment of FunCat numbers by homology alone is not always reliable, it may provide useful information in the absence of manual annotation. The automatic FunCat tables for all PEDANT databases were recalculated using the new FunCat version and updated manually annotated FunCat database. Figure 4 shows the FunCat distribution of all 334 genomes in PEDANT.