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Publikováno v:
Biology Direct, Vol 6, Iss 1, p 21 (2011)
Abstract Background Period 10 dinucleotides are structurally and functionally validated factors that influence the ability of DNA to form nucleosomes, histone core octamers. Robust identification of periodic signals in DNA sequences is therefore requ
Externí odkaz:
https://doaj.org/article/bc567948f492474fab1ffb775e831b36
Publikováno v:
Biology Direct, Vol 4, Iss 1, p 10 (2009)
Abstract Correction to Lindsay H, Yap VB, Ying H, Huttley GA: Pitfalls of the most commonly used models of context dependent substitution. Biology Direct 2008, 3:52
Externí odkaz:
https://doaj.org/article/a55b38d69ad14635a2e57f0a82092b67
Autor:
Huttley Gavin A, Hunter Lawrence, Easton Brett C, Smit Sandra, Caporaso J Gregory, Knight Rob
Publikováno v:
BMC Evolutionary Biology, Vol 8, Iss 1, p 327 (2008)
Abstract Background Identifying coevolving positions in protein sequences has myriad applications, ranging from understanding and predicting the structure of single molecules to generating proteome-wide predictions of interactions. Algorithms for det
Externí odkaz:
https://doaj.org/article/eca326d8793c4adbb9d300a4bf671506
Publikováno v:
BMC Bioinformatics, Vol 9, Iss 1, p 550 (2008)
Abstract Background Continuous-time Markov models allow flexible, parametrically succinct descriptions of sequence divergence. Non-reversible forms of these models are more biologically realistic but are challenging to develop. The instantaneous rate
Externí odkaz:
https://doaj.org/article/067e2450b0474d1c9cf00ae5857f08a3
Autor:
Huttley Gavin A, Yap Von Bing, McDonald Daniel, Oscamou Maribeth, Lladser Manuel E, Knight Rob
Publikováno v:
BMC Bioinformatics, Vol 9, Iss 1, p 511 (2008)
Abstract Background The nucleotide substitution rate matrix is a key parameter of molecular evolution. Several methods for inferring this parameter have been proposed, with different mathematical bases. These methods include counting sequence differe
Externí odkaz:
https://doaj.org/article/78633f65f64341e7bbde8cbe88c59909
Publikováno v:
Biology Direct, Vol 3, Iss 1, p 52 (2008)
Abstract Background Neighboring nucleotides exert a striking influence on mutation, with the hypermutability of CpG dinucleotides in many genomes being an exemplar. Among the approaches employed to measure the relative importance of sequence neighbor
Externí odkaz:
https://doaj.org/article/2c5e191347ce4df090cd78bfa5ed0120
Publikováno v:
BMC Bioinformatics, Vol 6, Iss 1, p 130 (2005)
Abstract Background Phylogenetic footprinting is the identification of functional regions of DNA by their evolutionary conservation. This is achieved by comparing orthologous regions from multiple species and identifying the DNA regions that have div
Externí odkaz:
https://doaj.org/article/2cfba4e0a1ae404f99cf6c39375822a0
Autor:
Wakefield Matthew J, Lawrence Cath, Lang Edward, Vedagiri Vivek, Butterfield Andrew, Isaev Alexander, Huttley Gavin A
Publikováno v:
BMC Bioinformatics, Vol 5, Iss 1, p 1 (2004)
Abstract Background Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of se
Externí odkaz:
https://doaj.org/article/5f602998eee74df68f8d33e34b059982
Autor:
Adcock, Gregory J., Dennis, Elizabeth S., Easteal, Simon, Huttley, Gavin A., Jermiin, Lars S., Peacock, W. James, Thorne, Alan
Publikováno v:
Proceedings of the National Academy of Sciences of the United States of America, 2001 Jan . 98(2), 537-542.
Externí odkaz:
https://www.jstor.org/stable/3054718