Building Block and Building Rule: Dual Descriptor Method for Biological Sequence Analysis

The emergence of “Systems Biology” in recent years highlights the systematic viewpoint of bio-system modeling. Building on such a background, Dual Descriptor Method, a generic methodology for biological sequence analysis is proposed. From a systematic perspective, Dual Descriptor is defined as a two element set of Composition Weight Map and Position Weight Function which aim at reflecting the composition and permutation information of a sequence. An alternate training algorithm is provided to get an optimum description of the building patterns of the sequences. In this paper, dual descriptor method has been applied to the analysis of two typical problems of molecular biology: gene identification and the prediction of protein function. Satisfactory and insightful results are achieved. Owing to the generality of this methodology, dual descriptor method has wide application perspective for many problems of pattern recognition, especially those involved in “Systems Biology”

Nucleon sea in the effective chiral quark model

The asymmetries of both light-flavor antiquark $\bar{d}(x)-\bar{u}(x)$ and strange-antistrange $s(x)-\bar{s}(x)$ distributions of the nucleon sea are considered with more details in the effective chiral quark model. We find that the asymmetric distribution of light-flavor antiquarks $\bar{d}(x)-\bar{u}(x)$ matches the experiment data well and that the asymmetry of strange and antistrange distributions can bring about 60-100% correction to the NuTeV anomaly of $\sin^{2}\theta_{w}$, which are three standard deviations from the world average value measured in other electroweak processes. The results on the correction to the NuTeV anomaly are insensitive to the inputs of the constituent quark distributions and the cut-off parameters. The ratios of $\bar{d}(x)/\bar{u}(x)$ and $s(x)/\bar{s}(x)$ are also discussed, and it is found that the ratio $s(x)/\bar{s}(x)$ is compatible with the available experiments with an additional symmetric sea contribution being considered effectively.Comment: 24 Latex pages, 8 figure

FDserver: A web service for protein folding research

*Summary:* To facilitate the study of protein folding, we have developed a web service for protein folding rate and folding type prediction as well as for the calculation of a variety of topological parameters of protein structure, which is freely available to the community.
*Availability:* http://sdbi.sdut.edu.cn/FDserve