Owen Z Woody,Andrew C Doxey,Brendan J McConkey
Owen Z Woody
Classical studies of the evolution of gene function have predominantly focused on mutations within protein coding regions. With the advent of microarrays, however, it has become possible to evaluate the transcriptional activity of a gene as...
Strategies for reliable exploitation of evolutionary concepts in high throughput biology [0.03%]
高通量生物学中可靠利用进化概念的战略方法学研究
Anthony Levasseur,Pierre Pontarotti,Olivier Poch et al.
Anthony Levasseur et al.
The recent availability of the complete genome sequences of a large number of model organisms, together with the immense amount of data being produced by the new high-throughput technologies, means that we can now begin comparative analyses...
Francisca C Almeida,Magdalena Leszczyniecka,Paul B Fisher et al.
Francisca C Almeida et al.
Details of the genomic changes that occurred in the ancestors of Eukarya, Archaea and Bacteria are elusive. Ancient interdomain horizontal gene transfer (IDHGT) amongst the ancestors of these three domains has been difficult to detect and a...
Chen-Hsiang Yeang
Chen-Hsiang Yeang
Many methods have been developed to detect coevolution from aligned sequences. However, all the existing methods require a one-to-one mapping of candidate coevolving partners (nucleotides, amino acids) a priori. When two families of sequenc...
David A Morrison
David A Morrison
The use of molecular sequence data has increased interest in trying to date evolutionary events, with researchers wanting both an estimate of the divergence time and a confidence interval for that estimate. However, two methodological issue...
The ABCs of MGR with DCJ [0.03%]
带DCJ的MGR的ABC
Zaky Adam,David Sankoff
Zaky Adam
We study the small phylogeny problem in the space of multichromosomal genomes under the double cut and join metric. This is similar to the existing MGR (multiple genome rearrangements) approach but it allows, in addition to inversion and re...
Mareike Fischer,Mike Steel
Mareike Fischer
The problem of intermediates in the fossil record has been frequently discussed ever since Darwin. The extent of 'gaps' (missing transitional stages) has been used to argue against gradual evolution from a common ancestor. Traditionally, ga...
Comparative evolutionary histories of the fungal chitinase gene family reveal non-random size expansions and contractions due to adaptive natural selection [0.03%]
真菌几丁质酶基因家族的比较进化历史揭示了适应性自然选择引起的非随机大小扩张和收缩
Magnus Karlsson,Jan Stenlid
Magnus Karlsson
Gene duplication and loss play an important role in the evolution of novel functions and for shaping an organism's gene content. Recently, it was suggested that stress-related genes frequently are exposed to duplications and losses, while g...
A simple derivation of the distribution of pairwise local protein sequence alignment scores [0.03%]
一对一的局部蛋白质序列比对得分分布的一个简单推导方法
Olivier Bastien
Olivier Bastien
Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. In the asymptotic limit of long sequences, the Karlin-Altschul model...
Francisco M Codoñer,Mario A Fares
Francisco M Codoñer
Non-independent evolution of amino acid sites has become a noticeable limitation of most methods aimed at identifying selective constraints at functionally important amino acid sites or protein regions. The need for a generalised framework ...