Modeling protein families using probabilisti suÆx trees
نویسندگان
چکیده
منابع مشابه
Protein Family Classi cation using Sparse Markov Transducers
In this paper we present a method for classifying proteins into families using sparse Markov transducers (SMTs). Sparse Markov transducers, similar to probabilistic suÆx trees, estimate a probability distribution conditioned on an input sequence. SMTs generalize probabilistic suÆx trees by allowing for wild-cards in the conditioning sequences. Because substitutions of amino acids are common in ...
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Abstra t. We present a rst formal setting for suÆx ve tors that are spa e e onomi al alternative data stru tures to suÆx trees. We give two linear algorithms for onverting a suÆx tree into a suÆx ve tor and onversely. We enri h suÆx ve tors with formulas for ounting the number of o urren es of repeated substrings. We also propose an alternative implementation for suÆx ve tors that should outper...
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Abstra t. In 1990 Manber & Myers proposed suÆx arrays as a spa e-saving alternative to suÆx trees and des ribed the rst algorithms for suÆx array onstru tion and use. Sin e that time, and espe ially in the last few years, sufx array onstru tion algorithms have proliferated in bewildering abundan e. This survey paper attempts to provide simple high-level des riptions of these numerous algorithms...
متن کاملModeling protein families using probabilistic su x trees
We present a method for modeling protein families by means of probabilistic suux trees (PSTs). The method is based on identifying signiicant patterns in a set of related protein sequences. The input sequences do not need to be aligned, nor is delineation of domain boundaries required. The method is automatic, and can be applied, without assuming any preliminary biological information, with surp...
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Abstra t. The spa e requirement of Cro hemore's repetitions algorithm is generally estimated to be about 20MN bytes of memory, where N is the length of the input string and M the number of bytes required to store the integer N . The same algorithm an also be used in other ontexts, for instan e to ompute the suÆx tree of the input string in O(N logN) time for the purpose of data ompression. In s...
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