M. Li, J.H. Badger, X. Chen, S. Kwong, P. Kearney, and H. Zhang, An information-based sequence distance and its application to whole mitochondrial genome phylogeny, Bioinformatics, 17:2(2001), 149--154.  Home/Search   Document Details and Download   Summary   Related Articles   Check

..... x n ) y 1 , y n ) t i=1 p(x i y i Other models are more complicated and take into account correlations across multiple nucleotides to model evolutionary patterns such as mutation variance among coding vs. non coding sites, codon position bias, etc. Consult [53] 36] or [33] for a more thorough treatment. 2.2 Computational Methods Most computational algorithms for solving the phylogenetic inference problem proposed throughout the years can be characterized by whether they explicitly incorporate the model of evolution into their inference procedure, or employ some ....

....distances. Pairwise evolutionary distances between sequences can be estimated by adopting some sequence based model of evolution such as Jukes Cantor [28] Kimura Two, etc. Note that this approach requires that the extant set S be an aligned set of gene sequences. Other approaches such as [33] uses an information theoretic estimate of the pair wise evolutionary distances between a set S of whole genomes, rather than a set of aligned sequences. Figure (7) illustrates the high level idea behind distance based methods. 2.4.1 Neighbour Joining Neighbour Joining (NJ) 45] is a greedy, ....

[Article contains additional citation context not shown here]

Li, M., Badger, J., Xin, C., Kwong, S., Kearney, P., and Zhang, H. An information based sequence distance and its applications to whole genome mitochondrial phylogeny. Bioinformatics (2001). 88

....differing evolutionary rates can result in phylogenetic trees with the wrong topology. The recently completed sequences of several organism genomes provide an enormous amount of data with which to address some of these problems. Phylogenetic analysis can also be performed using the whole genome [14, 29], leading to more precise studies. However, only a limited number of genome sequences are available to date, and hence the results of such techniques may not be representative of the whole picture. 2.2 Phylogenetic trees based on metabolic pathways Metabolism is defined as the set of complex ....

Ming Li, Jonathan H. Badger, Xin Chen, Sam Kwong, Paul Kearney, and Haoyong Zhang. An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics, 17:149--154, 2001.

No context found.

M. Li, J.H. Badger, X. Chen, S. Kwong, P. Kearney, and H. Zhang, An information-based sequence distance and its application to whole mitochondrial genome phylogeny, Bioinformatics, 17:2(2001), 149--154.

No context found.

M. Li, J.H. Badger, X. Chen, S. Kwong, P. Kearney, and H. Zhang, An information-based sequence distance and its application to whole mitochondrial genome phylogeny, Bioinformatics, 17:2(2001), 149--154.

No context found.

M. Li, J. Badger, X. Chen, S. Kwong, P. Kearney and H. Zhang. An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics. 17:2(2001), 149-154.

No context found.

Li, M., Badger, J., Xin, C., Kwong, S., Kearney, P., and Zhang, H. An information based sequence distance and its applications to whole genome mitochondrial phylogeny. Bioinformatics (2001). 87

....in student programming assignments [32] and phylogeny of chain letters in [5] We plan a further test on arti cially generated data, where we know the right answer beforehand. Related Work: Together with our coauthors, we have studied various forms of information distance in [4] and [21] in the past. The information distance studied in [23, 4] and subsequently investigated in [22, 16, 26, 28, 35] is universal and has other nice properties. This distance essentially says that the distance between two objects is the length of the shortest program (or amount of energy) that is ....

....compression distance. Both of these measures are essentially K(xjy) Other than being asymmetric, they also su er similar problems as the information distance of [4] as show in the above example. Preliminary applications of the current approach were tentatively reported to the biological community [21] using an initial and partially improper distance. Subsequent work in the linguistics community, 2, 3] inferred a language tree from di erent language text corpora, as well as attributed authorship on basis of text corpora. Their methods are compression based on a certain type of empirical ....

[Article contains additional citation context not shown here]

M. Li, J.H. Badger, X. Chen, S. Kwong, P. Kearney, and H. Zhang, An information-based sequence distance and its application to whole mitochondrial genome phylogeny, Bioinformatics, 17:2(2001), 149-154.

....between 0 and 1. It is known that this metric may be greatly plagued due to the incapability of dynamic programming technique to deal with transposed code segments. 3 Shared information An information based sequence distance to measure similarity between sequence pairs was first proposed in [7, 4], and has been successfully applied to the construction of whole genome phylogenies [7] chain letter evolutionary history [3] and language classification [2, 5] Its definition is based Kolmogorov complexity or algorithmic entropy [8] The Kolmogorov complexity of string s, K(s) measures ....

....of dynamic programming technique to deal with transposed code segments. 3 Shared information An information based sequence distance to measure similarity between sequence pairs was first proposed in [7, 4] and has been successfully applied to the construction of whole genome phylogenies [7], chain letter evolutionary history [3] and language classification [2, 5] Its definition is based Kolmogorov complexity or algorithmic entropy [8] The Kolmogorov complexity of string s, K(s) measures the amount of absolute information content a sequence s contains. In other words, K(s) is ....

[Article contains additional citation context not shown here]

M. Li, J. Badger, X. Chen, S. Kzong, P. Kearney and H. Zhang. An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics. 17:2(2001), 149-154.

....all clearly having a common ancestry with the English language letters. These were excluded from the study because we doubted their degree of similarity could be adequately assessed by our algorithms. To compute the distance between chain letters x and y, we used a new distance measure defined in [4, 11]: d(x; y) 1 Gamma K(x) K(y) Gamma K(xy) K(xy) where K(x) is the algorithmic entropy (Kolmogorov complexity) of the string x, ie the the length in bits of the shortest program causing a standard universal computer to compute x as its unique output. The numerator of the fraction is the ....

....mutual algorithmic information between x and y, equal (to within a logarithmic error term [12] to the number of bits x tells about how to compute y, or vice versa. Mutual algorithmic information is not itself a distance and does not satisfy the triangle inequality, but d(x; y) defined above does[11], ranging from a minimum of 0 when x = y to a maximum of 1 when x and y are independent strings of equal or differing length. By contrast with our present d, the Information Distance defined in [2] can become arbitrarily large, and thus is not suitable in the present aplication because it would ....

[Article contains additional citation context not shown here]

Li, M., Chen, X., Badger, J., Kwong, S., Kearney, P., & Zhang, H., An information based sequence distance and its application to whole genome phylogeny. Manuscript, 1999.

....compare genomes. Traditional approaches of computing the phylogeny use so called multiple alignment. They would not work here since chain letters contain swapped sentences and genomes contain translocated genes and noncoding regions. Using the chain letter method, a more serious application in [1] automatically builds correct phylogenies from complete mitochondrial genomes of mammals. We con rmed a biological conjecture that ferungulates placental mammals that are not primates, including cats, cows, horses, whales are closer to the primates monkeys, humans than to rodents. Inductive ....

M. Li, J.H. Badger, X. Chen, S. Kwong, P. Kearney, and H. Zhang, An information-based sequence distance and its application to whole mitochondrial genome phylogeny, Bioinformatics, 17:2(2001), 149-154.

No context found.

M. Li, J.H. Badger, X. Chen, S. Kwong, P. Kearney, and H. Zhang, An information-based sequence distance and its application to whole mitochondrial genome phylogeny, Bioinformatics, 17:2(2001), 149--154.

No context found.

M. Li, J.H. Badger, X. Chen, S. Kwong, P. Kearney, and H. Zhang. An information-based sequence distance and its application to whole mitochondrial genome phylogeny, Bioinformatics, 17:2(2001), 149--154.

No context found.

M. Li, J.H. Badger, X. Chen, S. Kwong, P. Kearney, and H. Zhang. An information-based sequence distance and its application to whole mitochondrial genome phylogeny, Bioinformatics, 17:2(2001), 149--154.

No context found.

M. Li, J. H. Badger, X. Chen, S. Kwong, P. Kearney, and H. Zhang. An informationbased sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics, 17(2):149--154, 2001.

No context found.

Li M. et al., (2001) An information-based sequence distance and its application to whole mitochondrial genome phylogeny, Bioinformatics 17, 149-154.

No context found.

Li, M. et al. (in press) An Information Based Sequence Distance and its Application to Whole Mitochondrial Genome Phylogeny. Bioinformatics.

Online articles have much greater impact   More about CiteSeer.IST   Add search form to your site   Submit documents   Feedback  

CiteSeer.IST - Copyright Penn State and NEC