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21.
Combining protein evolution and secondary structure 总被引:19,自引:9,他引:10
An evolutionary model that combines protein secondary structure and amino
acid replacement is introduced. It allows likelihood analysis of aligned
protein sequences and does not require the underlying secondary (or
tertiary) structures of these sequences to be known. One component of the
model describes the organization of secondary structure along a protein
sequence and another specifies the evolutionary process for each category
of secondary structure. A database of proteins with known secondary
structures is used to estimate model parameters representing these two
components. Phylogeny, the third component of the model, can be estimated
from the data set of interest. As an example, we employ our model to
analyze a set of sucrose synthase sequences. For the evolution of sucrose
synthase, a parametric bootstrap approach indicates that our model is
statistically preferable to one that ignores secondary structure.
相似文献
22.
Chun-Nan Hsu Jin-Mei Lai Chia-Hung Liu Huei-Hun Tseng Chih-Yun Lin Kuan-Ting Lin Hsu-Hua Yeh Ting-Yi Sung Wen-Lian Hsu Li-Jen Su Sheng-An Lee Chang-Han Chen Gen-Cher Lee DT Lee Yow-Ling Shiue Chang-Wei Yeh Chao-Hui Chang Cheng-Yan Kao Chi-Ying F Huang 《BMC bioinformatics》2007,8(1):1-12
Background
An adequate and expressive ontological representation of biological organisms and their parts requires formal reasoning mechanisms for their relations of physical aggregation and containment.Results
We demonstrate that the proposed formalism allows to deal consistently with "role propagation along non-taxonomic hierarchies", a problem which had repeatedly been identified as an intricate reasoning problem in biomedical ontologies.Conclusion
The proposed approach seems to be suitable for the redesign of compositional hierarchies in (bio)medical terminology systems which are embedded into the framework of the OBO (Open Biological Ontologies) Relation Ontology and are using knowledge representation languages developed by the Semantic Web community. 相似文献23.
Richardson TI Frank SA Wang M Clarke CA Jones SA Ying BP Kohlman DT Wallace OB Shepherd TA Dally RD Palkowitz AD Geiser AG Bryant HU Henck JW Cohen IR Rudmann DG McCann DJ Coutant DE Oldham SW Hummel CW Fong KC Hinklin R Lewis G Tian H Dodge JA 《Bioorganic & medicinal chemistry letters》2007,17(13):3544-3549
Structure-activity relationship studies are described, which led to the discovery of novel selective estrogen receptor modulators (SERMs) for the potential treatment of uterine fibroids. The SAR studies focused on limiting brain exposure and were guided by computational properties. Compounds with limited impact on the HPO axis were selected using serum estrogen levels as a biomarker for ovarian stimulation. 相似文献
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25.
Arthur Chun-Chieh Shih DT Lee Laurent Lin Chin-Lin Peng Shiang-Heng Chen Yu-Wei Wu Chun-Yi Wong Meng-Yuan Chou Tze-Chang Shiao Mu-Fen Hsieh 《BMC bioinformatics》2006,7(1):103-15
Background
Deluged by the rate and complexity of completed genomic sequences, the need to align longer sequences becomes more urgent, and many more tools have thus been developed. In the initial stage of genomic sequence analysis, a biologist is usually faced with the questions of how to choose the best tool to align sequences of interest and how to analyze and visualize the alignment results, and then with the question of whether poorly aligned regions produced by the tool are indeed not homologous or are just results due to inappropriate alignment tools or scoring systems used. Although several systematic evaluations of multiple sequence alignment (MSA) programs have been proposed, they may not provide a standard-bearer for most biologists because those poorly aligned regions in these evaluations are never discussed. Thus, a tool that allows cross comparison of the alignment results obtained by different tools simultaneously could help a biologist evaluate their correctness and accuracy. 相似文献26.
Baltz R Domon C Pillay DT Steinmetz A 《The Plant journal : for cell and molecular biology》1992,2(5):705-711
The maize transposable element Activator (Ac) carries subterminal CpG-rich sequences which are essential for the transposition of the element. It has previously been shown that the methylation of certain sequences contained in this region can alter their ability to interact with the Ac-encoded protein. The novel hypothesis that the methylation of subterminal Ac sequences is required for transposition was tested. Approximately 150 bp of the 5' subterminal region of the Ac element was examined for the presence of 5-methylcytosines by the ligation-mediated polymerase chain reaction (LMPCR)-aided genomic sequencing method. The methylation status of 22 and 39 cytosines on either strand of the DNA were analysed in each of five different transgenic tobacco cultures carrying transposable Ac sequences. Ten micrograms of tobacco DNA were used for each base-specific cleavage reaction before amplification by LMPCR. All but one of the cytosines were unmethylated. Only a minor fraction of the Ac molecules was methylated at one cytosine residue. It is concluded that DNA methylation at the tested Ac sequences is not required for the transposability of Ac or Ds elements in tobacco cells. 相似文献