This allows the prediction of GPIanchored protein using knowledge-based algorithm. There are 24,725 predicted protein-coding genes in T. thermophila MAC genome. The majority of the genes in T. thermophila are transcriptionally regulated as determined by nuclear run-on assay. Post-transcriptional control via mRNA stability was also observed in SerH3 gene regulation. As the Ser gene family is highly polymorphic, sequence homology analysis alone 
cannot recognize the full set of putative Ser genes. In order to gain a full understanding of the antigenic variation in T. thermophila Ser genes, it is necessary to overcome this problem. In this study, the repertoire of the T. thermophila Ser gene family was annotated by setting search criteria based on the repetitive cysteine-rich motif and the signal sequence for GPI anchor. Putative Ser genes were further characterized based on their phylogenetic distribution with experimentally classified Ser subtypes. By combining the data from the Ser candidates and the known Ser genes, the patterns of Ser chromosomal localization and gene expression were revealed. In this study, an alternative strategy was adopted for identifying this gene family by selecting two common features of the known Ser genes, namely, the Cys-rich motif and GPI-anchor site. Their phylogenetic distributions were analyzed in order to characterize Ser candidates that are related to the known subtypes. The approach identified Ser candidates that can be grouped into the known subtypes. However, 55% of the genes could not be classified into any known subtype based on phylogenetic analysis, and might belong to new subtypes. At present, the genes encoding several types of surface antigens such as SerT, SerS, SerM and SerI have not been identified indicating the existence of more Ser repertoires and subtypes. In addition, certain unclassified gene candidates exhibit properties similar to Ser, such as tendency to be located in tandem and have similar gene expression profile. It is possible that the missing Ser Albaspidin-AA subtypes might belong to one of the unclassified gene families. Experiments with specific antibodies to Ser candidates will be required in order to prove that they are indeed i-ag proteins. Sequence comparison and synteny analysis of the highly polymorphic Ser genes from more T. thermophila isolates will confirm whether these genes are under positive selection which is a strong evolutionary driving force for mating proteins, Homatropine Bromide molecular sensors and evasive decoys. Using the Ser candidates as blastp query on NCBI protein database yields sixteen T. thermophila proteins not previously included in the list. Nevertheless, they either lack the GPI anchor motif or matching cysteine pattern. The phylogenetic analysis showed that these proteins are not grouped with any Ser candidate. The analysis outside T. thermophila revealed two weak hits with the proteins from other ciliates. This might indicate that the Ser gene family is unique to T. thermophila. i-ag proteins were discovered based on their variation in response to antibodies directed at T. thermophila surface antigens. This is a hallmark for many antigenic variation phenomena among parasitic and free-living protozoa. In parasitic protozoa such as Plasmodium falciparum, a family of proteins on infected red blood cells is needed for a parasitic adherence mechanism to human cells and tissue which is crucial for malaria pathogenesis.