02189nas a2200181   4500008004100000022001400041245010700055210006900162260007200231300001400303490000700317520147000324100002401794700001701818700002101835700002301856856012801879       2013                        eng d  a0305-104800aOne size does not fit all: on how markov model order dictates performance of genomic sequence analyses0 aOne size does not fit all on how markov model order dictates per  aGREAT CLARENDON ST, OXFORD OX2 6DP, ENGLANDbOXFORD UNIV PRESScFEB  a1416-14240 v413 a<p>The structural simplicity and ability to capture serial correlations make Markov models a popular modeling choice in several genomic analyses, such as identification of motifs, genes and regulatory elements. A critical, yet relatively unexplored, issue is the determination of the order of the Markov model. Most biological applications use a predetermined order for all data sets indiscriminately. Here, we show the vast variation in the performance of such applications with the order. To identify the `optimal' order, we investigated two model selection criteria: Akaike information criterion and Bayesian information criterion (BIC). The BIC optimal order delivers the best performance for mammalian phylogeny reconstruction and motif discovery. Importantly, this order is different from orders typically used by many tools, suggesting that a simple additional step determining this order can significantly improve results. Further, we describe a novel classification approach based on BIC optimal Markov models to predict functionality of tissue-specific promoters. Our classifier discriminates between promoters active across 12 different tissues with remarkable accuracy, yielding 3 times the precision expected by chance. Application to the metagenomics problem of identifying the taxum from a short DNA fragment yields accuracies at least as high as the more complex mainstream methodologies, while retaining conceptual and computational simplicity.</p>1 aNarlikar, Leelavati1 aMehta, Nidhi1 aGalande, Sanjeev1 aArjunwadkar, Mihir  uhttps://library.ncl.res.in/content/one-size-does-not-fit-all-how-markov-model-order-dictates-performance-genomic-sequence-0