Effects of Mapping Methods on Accuracy of Protein Coding Regions Prediction

[Objective] To discuss the effects of major mapping methods for DNA sequence on the accuracy of protein coding regions prediction,and to find out the effective mapping methods.[Method] By taking Approximate Correlation（AC） as the full measure of the prediction accuracy at nucleotide level,the windowed narrow pass-band filter（WNPBF） based prediction algorithm was applied to study the effects of different mapping methods on prediction accuracy.[Result] In DNA data sets ALLSEQ and HMR195,the Voss and Z-Curve methods are proved to be more effective mapping methods than paired numeric（PN）,Electron-ion Interaction Potential（EIIP） and complex number methods.[Conclusion] This study lays the foundation to verify the effectiveness of new mapping methods by using the predicted AC value,and it is meaningful to reveal DNA structure by using bioinformatics methods.

MULTISTAGE FILTERS FOR IDENTIFICATION OF EUKARYOTIC PROTEIN CODING REGIONS

A class of multistage filters, namely, real narrowband bandpass filter （RNBPF） has been previously used for identification of protein coding regions. This filter passes the frequency component at 2π/3 along with its conjugate. This conjugate frequency compo- nent may degrade the identification accuracy. To improve the identification accuracy, two types of multistage filters are proposed in this paper. A complex narrowband bandpass filter （CNBPF） is proposed for suppressing the conjugate frequency component which, in turn, reduces the background noise present in the deoxyribonucleic acid （DNA） spec- trum and improves identification accuracy. By cascading RNBPF with moving average filter （RNBPFMA）, another type of multistage filter is proposed. As moving average filter smooth out the rapid variations in the DNA spectrum, RNBPFMA improves the identification accuracy. The computational complexity of RNBPFMA is less than that of CNBPF. The RNBPF and proposed multistage filters are compared with previously reported short-time discrete Fourier transform （ST-DFT） method in terms of compu- tational complexity. It is found that multistage filters reduce the computational load to a greater extent compared to ST-DFT method. The identification accuracy of the proposed CNBPF and RNBPFMA methods is compared with existing anti-notch filter and RNBPF methods. The results show that proposed methods outperform existing methods in terms of identification accuracy for benchmark data sets.

The Complete Genomic Sequence of a Foot-and-Mouth Disease Virus Isolated from the Swine

The complete genomic sequence of foot-and-mouth disease virus (FMDV) Chinese strain OH/CHA/99 was determined. The 8040 nt sequence and the deduced amino acid sequence werecompared with FMDV sequences published. The results showed that OH/CHA/99 shared highersequence homology with OTYTW/97, indicating their close genetic relationship. However,the strain had lower sequence identity with O1/Kaufbeuren/66 strain. Besides, largedeletions in 3A coding region were observed in OH/CHA/99. It was shown that the poly (A)tail of OH/CHA/99 had 56 As at least.

Study of Resistin gene expression in peripheral blood mononuclear cell and its gene polymorphism in a small range population

Objective: To observe the expression of Resistin mRNA in peripheral blood mononuclear cells and its gene poly-morphism in coding region in a small range population in Zhejiang Province of China. Methods: Eighty-three cases of type 2 diabetes mellitus and 53 healthy people were included. The expression of Resistin mRNA in peripheral blood mononuclear cells was detected by RT-PCR and semi-quantitative PCR assay. The sequencing work was done in Resistin cDNA and gene poly-morphism was analyzed. Results: At the same condition, in 83 diabetes patients, Resistin mRNA was detected in 23 cases (11 males and 12 females). There was no Resistin mRNA expression in 53 healthy people. The ratio of PCR products between Resistin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was from 0.564 to 1.238, averaging 0.804±0.436. The sequence of Resistin cDNA is almost identical with each other and with that in GenBank with no single nucleotide polymorphism being found. Conclusion: Resistin mRNA is expressed in human peripheral blood mononuclear cells in some type 2 diabetes mellitus, but its expression is at a low level. Among the experiment population we did not find polymorphism phenomenon in Resistin coding region. The different individual’s Resistin coding region is highly coincident.

Preparation and analysis of cSNP chip on hepatocellular carcinoma-related genes

The understanding of cSNPs of cancer-related genes harboring in high frequency loss regions of tumor chromosomes can advance the disclosure of genetic and variant mechanisms of tumorigenesis,and the investigation of cancer susceptibility. In preparing a gene chip for detecting polymorphisms on coding region of genes in hepatocellular carcinoma tissues, some cSNPs are of interest for their potential links with phenotype. METHODS: The genes harboring in loss regions with high frequency of hepatocellular carcinoma (HCC) were selected, the related information of cSNP sequences was obtained from the SNP database (dbSNP) of the National Center for Biotechnology Information (NCBI). Then appropriate primers and oligonucleotide probes were designed according to the SNP sites, and a gene chip for the detection of SNPs was constructed. The chip included 48 cSNPs of 25 hepatocellular carcinoma-related genes. The PCR products labeled by Dig-dUTP were hybridized with the cSNP chip. RESULTS:The sensitivity, influence by probe concentration, and reiteration of the chip were detected, with a high sensitivity of 6 × 10-3 ng/μl. The signal of hybridization was reduced with a lower concentration of probe. Seven polymorphisms of caspase 9 (rs2308941) C →T and DOK2 (rs2242241) T→G, 6 of polymorphisms of EGFL3 (rs947345) A→G, caspase 9 (rs2308938) C→G and PHGDH (rs1801955)T→A, 5 of polymorphisms of E2F2(rs3218170) G→A,4 of polymorphisms of MUTYH( rs1140507) T→C and BNIP3L(rs1055806)G→T, and 1 of polymorphism of TNFRSF1B (rs1061622)T→G were detected by the chip in the tissues of 10 HCC. Samples of caspase 9 (rs2308941G) and (rs2308941A) were verified by PCR-SSCP and sequencing. CONCLUSION:The cSNP chip of hepatocellular carcinoma-related genes can accelerate the discovery of polymorphic markers on hepatocellular carcinoma.

HiSC:A Hybrid XML Index Composing Structure-Encoded with Cluster

A new way of indexing and processing twig patterns in an XML documents is proposed in this paper. Every path in XML document can be transformed into a sequence of labels by Structure-Encoded that constructs a one-to-one correspondence between XML tree and sequence. Base on identifying characteristics of nodes in XML tree, the elements are classified and clustered. During query proceeding, the twig pattern is also transformed into its Structure-Encoded. By performing subsequence matching on the set of sequences in XML documents, all the occurrences of path in the XML documents are refined. Using the index, the numbers of elements retrieved are minimized. The search results with pertinent format provide more structure information without any false dismissals or false alarms. The index also supports keyword search Experiment results indicate the index has significantly efficiency with high precision.

Analysis of genotype polymorphism of tumor-related genes harbored in chromosome arm 1p and 8p in hepatocellular carcinoma patients by cSNP chip

The majority of single nucleotide polymorphisms(SNPs)found in the coding region(cSNPs)are single base substitutions that may or may not lead to amino acid substitutions,most of which are related to diseases.Some cSNPs may prove useful for their potential links to functional cSNPs via linkage disequilibrium mapping.We have selected 48 cSNPs located in the coding regions of 25 genes to construct the cSNP chip.These genes are harbored in the high frequency loss regions of the chromosome 1p and 8p and related with apoptosis,cell cycles,signal transduction,oncogene,tumor suppressor genes and so on.All of the cSNPs can lead to amino acid substitutions except TP73(rs1801174).The PCR products amplified from 31 hepatocellular carcinoma(HCC)specimens were labeled with Dig-dUTP and then hybridized with the cSNP chips.The results showed that there was no hybridization signal when there was more than one site of mutation in the amplification sequence,indicating that the cSNP chip had a high sensitivity.The statistic data of the SNP(MT,homozygous and HT,heterozygous)in the HCC patients with different phenotypes(HBV+/-,differentiation stage,family history positive or negative,tumor size)indicated that the number of MT was distinctly different between patients with positive HBV and negative HBV.The MT and HT numbers of all the 48 cSNPs were significantly different between low differentiation and high differentiation HCC patients.The numbers of MT and HT were not different between positived and negative family history groups and between tumor size>3 cm and≤3 cm groups.The study results provided useful information for understanding the molecular mechanisms of HCC development.

Research on Holistic Index Method of Geography Markup Language

Currently, the OGC GML （Geography Markup Language） specification has been the de facto standard for GIS data sharing and exchanging and spatial interoperation. Adopting nested association expression approach of XML data, GML data documents can store both spatial information and semantic relationship information of geographical elements. To improve the efficiency of path query on GML two type information, the paper describes a holistic index method for GML data, which we call EKR^＋ （optimized R＋-tree base on Extend Region Code and K-means extent partition of GML feature elements）. The experiment results show that the efficiency of semantic-spatial query can be improved greatly by utilizing EKR^＋.