Discovery of Novel 4${\alpha}$ helix Cytokine by Hidden Markov Model Analysis

Cytokines play a crucial role in the immune and inflammatory responses. But because of the high evolutionary rate of these proteins, the similarity between different members of their family is very low, which makes the identification of novel members of cytokines very difficult. According to this point, a new bioinformatic strategy to identify novel cytokine of the short-chain and long-chain 4${\alpha}$ helix cytokine using hidden markov model (HMM) is proposed in the paper. As a result, two motifs were created on the two train data sets, which were used to search three different databases. In order to improve the result, a strict criterion is established to filter the novel cytokines in the subject proteins. Finally, according to their E-value, scores and the criterion, four subject proteins are predicted to be possible novel cytokines for each family respectively.