Stochastic Insertion-Deletion Processes and Statistical Sequence Alignment
نویسندگان
چکیده
1 FB Biologie und Informatik, Goethe-Universität, 60054 Frankfurt am Main, Germany, [email protected] 2 Department of Mathematics, University of Idaho, P.O. Box 441103. Moscow, ID 83844-1103, USA, [email protected] 3 FB Mathematik, Goethe-Universität, 60054 Frankfurt am Main, Germany, [email protected] 4 Bioinformatik, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany, [email protected] 5 Forschungszentrum Jülich, John von Neumann-Institut für Computing (NIC), Forschungsgruppe Bioinformatik, 52425 Jülich, Germany
منابع مشابه
Stochastic models of sequence evolution including insertion-deletion events.
Comparison of sequences that have descended from a common ancestor based on an explicit stochastic model of substitutions, insertions and deletions has risen to prominence in the last decade. Making statements about the positions of insertions-deletions (abbr. indels) is central in sequence and genome analysis and is called alignment. This statistical approach is harder conceptually and computa...
متن کاملStatistical alignment based on fragment insertion and deletion models
MOTIVATION The topic of this paper is the estimation of alignments and mutation rates based on stochastic sequence-evolution models that allow insertions and deletions of subsequences ('fragments') and not just single bases. The model we propose is a variant of a model introduced by Thorne et al., (J. Mol. Evol., 34, 3-16, 1992). The computational tractability of the model depends on certain re...
متن کاملBayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model
A central problem in computational biology is the inference of phylogeny given a set of DNA or protein sequences. Currently, this problem is tackled stepwise, with phylogenetic reconstruction dependent on an initial multiple sequence alignment step. However these two steps are fundamentally interdependent. Whether the main interest is in sequence alignment or phylogeny, a major goal of computat...
متن کاملRose: generating sequence families
MOTIVATION We present a new probabilistic model of the evolution of RNA-, DNA-, or protein-like sequences and a software tool, Rose, that implements this model. Guided by an evolutionary tree, a family of related sequences is created from a common ancestor sequence by insertion, deletion and substitution of characters. During this artificial evolutionary process, the 'true' history is logged an...
متن کاملUsing evolutionary Expectation Maximisation to estimate indel rates
Motivation: The Expectation Maximisation algorithm, in the form of the Baum-Welch algorithm (for HMMs) or the Inside-Outside algorithm (for SCFGs), is a powerful way to estimate the parameters of stochastic grammars for biological sequence analysis. To use this algorithm for multiplesequence evolutionary modeling, it would be useful to apply the EM algorithm to estimate not just the probability...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره شماره
صفحات -
تاریخ انتشار 2004