Journal of Applied Sciences1812-56541812-5662Asian Network for Scientific Information10.3923/jas.2012.1518.1525MajiSrabanti GargDeepak 1220121215The objective of this study is to perform mini review on Hidden
Markov Models (HMMs) which is recently important and popular among bioinformatics
researchers and large no of software tools are based on this technique. The
mathematical foundations of HMMs shall be considered first in brief manner and
then the gene identification application. In the case of gene identification
process, HMM basically resolve three basic problems: First is the evaluation
problem, in this it computes the probability that a particular HMM will generates
a given sequence of observations. Second is Decoding problem, in which it will
uncover the most likely hidden state and Third is Learning problem, it is used
to adjust the model parameter and train the HMM to find an optimal model. Evaluation
problem can be solved by using Forward and Backward algorithm, Decoding problems
are solved by using Viterbi algorithm and posterior decoding algorithm and then
Learning problems are solved through Viterbi training algorithm and Baum-Welch
algorithm. Finally, some limitations of the current approaches and future directions
are also reported.]]>Parent, A., I. Benzaghou, I. Bougie and M. Bisaillon,20044624627Larik, A.S. and Z.A. Soomro,20032551560Birney, E.,200145449454Borodovsky, M. and J. McIninch,199317123133Burge, C. and S. Karlin,19972687894Burge, C.B. and S. Karlin,19988346354Cawley, S.L. and L. Pachter,200319ii36ii41De Fonzo, V., F. Aluffi-Pentini and V. Parisi,200724961Nath, D.C. and A. Bhattacharjee,20114640648Durbin, R., S. Eddy, A. Krogh and G. Mitchison,1998Eddy, S.R.,20042213151316Garg, D.,20072007Garg, D.,20071339346Henderson, J., S. Salzberg and K.H. Fasman,19974127141Nasiri, J., A. Haghnazari and M. Alavi,201141022Cheng, K. and C.H. Zou,20072432436Kim, J.S.,2006Arabidopsis thaliana.]]>22328Krogh, A., I.S. Mian and D. Haussler,1994Escherichia coli DNA.]]>2247684778Kulp, D., D. Haussler, M.G. Reese and F.H. Eeckman,19964134142Kumar, M. and G.P.S. Raghava,20092009Lee, S.A., C.H. Chan, C.H. Tsai, J.M. Lai, F.S. Wang, C.Y. Kao and C.Y.F. Huang,20082008Jing, L., H. Hua and L. Sufang,200617982Lifshits, Y., S. Mozes, O. Weimann and M. Ziv-Ukelson,200954379399Lukashin, A.V. and M. Borodovsky,19982611071115Lunter, G.,20072324852487Frikha, M., Z.B. Messaoud and A.B. Hamida,2007738913899Majoros, W.H., M. Pertea and S.L. Salzberg,20052117821788Meyer, I.M. and R. Durbin,2002ab initio prediction of gene structures using pair HMMs.]]>1813091318Dosay-Akbulut, M.,20066921925El-Sayed, M.H. and A.M. Khedr,2007716261632Ahmad, M., A. Abdullah and K. Buragga,201111806814Oron, A.P., Z. Jiang and R. Gentleman,20082425862591Pop, M. and S.L. Salzberg,200824142149Rabiner, L.,198977257286Sur, S., M. Bhattacharya, A.K. Bothra, L.S. Tisa and A. Sen,2008Azotobacter vinelandii.]]>7242249Tran, D.H., K. Satou and T.B. Ho,20082008Tran, T.T., F. Zhou, S. Marshburn, M. Stead, S.R. Kushner and Y. Xu,2009De novo computational prediction of non-coding RNA genes in prokaryotic genomes.]]>2528972905Wang, X., D. Wu, S. Zheng, J. Sun, L. Tao, Y. Li and Z. Cao,20082008Yang, J.Y. and M.Q. Yang,20082121133Yoon, B.J. and P.P. Vaidynathan,2004216511655Pedersen, J.S. and J. Hein,200319219227Bhardwaj, L.M., D. Garg and S.C. Saxena,200722936