000077235 001__ 77235
000077235 005__ 20181203020112.0
000077235 0247_ $$2doi$$a10.1016/S0097-8485(96)80003-9
000077235 037__ $$aARTICLE
000077235 245__ $$aA flexible motif search technique based on generalized profiles
000077235 269__ $$a1996
000077235 260__ $$c1996
000077235 336__ $$aJournal Articles
000077235 500__ $$aPRO 96.11
000077235 520__ $$aA flexible motif search technique is presented which has two major components: (1) a generalized profile syntax serving as a motif definition languaje; and (2) a motif search method specifically adapted to the problem of finding multiple instances of a motif in the same sequence.The new profile structure, which is the core of the generalized profile syntax, combines the functions of a variety of motif descriptors implemented in other methods, including regular expression-like patterns, weight matrices, previously used profiles, and certain types of hidden Markov models (HMMs). The relationship between generalized profiles and other biomolecular motif descriptors is analyzed in detail, with special attention to HMMs. Generalized profiles are shown to be equivalent to a particular class of HMMs, and conversion procedures in both directions are given. The conversion procedures provide an interpretation for local alignement in the framework of stochastic models, allowing for clear, simple significance test. A mathematical statement of the motif search problems defines the new method exactly without linking it to a specific algorithmic solution. Part of the definition includes a new definition of disjointness of alignements.
000077235 700__ $$0244404$$g113607$$aBucher, P.
000077235 700__ $$aKarplus, K.
000077235 700__ $$aMoeri, N.
000077235 700__ $$aHofmann, K.
000077235 773__ $$j20$$tComputers Chem.$$k1$$q3-23
000077235 909C0 $$0252055$$pROSO
000077235 909C0 $$pGR-BUCHER$$xU11780$$0252244
000077235 909CO $$pSV$$particle$$ooai:infoscience.tind.io:77235
000077235 937__ $$aROSO-ARTICLE-1996-002
000077235 970__ $$aBucher1996_501/ROSO
000077235 973__ $$sPUBLISHED$$aEPFL
000077235 980__ $$aARTICLE