Chaos game representation （CGR） is an iterative mapping technique that processes sequences of units, such as nucleotides in a DNA sequence or amino acids in a protein, in order to determine the coordinates of their ...Chaos game representation （CGR） is an iterative mapping technique that processes sequences of units, such as nucleotides in a DNA sequence or amino acids in a protein, in order to determine the coordinates of their positions in a continuous space. This distribution of positions has two features： one is unique, and the other is source sequence that can be recovered from the coordinates so that the distance between positions may serve as a measure of similarity between the corresponding sequences. A CGR-walk model is proposed based on CGR coordinates for the DNA sequences. The CGR coordinates are converted into a time series, and a long-memory ARFIMA （p, d, q） model, where ARFIMA stands for autoregressive fractionally integrated moving average, is introduced into the DNA sequence analysis. This model is applied to simulating real CGR-walk sequence data of ten genomic sequences. Remarkably long-range correlations are uncovered in the data, and the results from these models are reasonably fitted with those from the ARFIMA （p, d, q） model.展开更多
A new chaos game representation of protein sequences based on the detailed hydrophobic-hydrophilic （HP） model has been proposed by Yu et al （Physica A 337（2004） 171）. A CGR-walk model is proposed based on the ne...A new chaos game representation of protein sequences based on the detailed hydrophobic-hydrophilic （HP） model has been proposed by Yu et al （Physica A 337（2004） 171）. A CGR-walk model is proposed based on the new CGR coordinates for the protein sequences from complete genomes in the present paper. The new CCR coordinates based on the detailed HP model are converted into a time series, and a long-memory ARFIMA（p, d, q） model is introduced into the protein sequence analysis. This model is applied to simulating real CCR-walk sequence data of twelve protein sequences. Remarkably long-range correlations are uncovered in the data and the results obtained from these models are reasonably consistent with those available from the ARFIMA（p, d, q） model.展开更多
An effective approach, mapping the texture for building model based on the digital photogrammetric theory, is proposed. The easily-acquired image sequences from digital video camera on helicopter are used as texture r...An effective approach, mapping the texture for building model based on the digital photogrammetric theory, is proposed. The easily-acquired image sequences from digital video camera on helicopter are used as texture resource, and the correspondence between the space edge in building geometry model and its line feature in image sequences is determined semi-automatically. The experimental results in production of three-dimensional data for car navigation show us an attractive future both in efficiency and effect.展开更多
Forecasting subtle traps by sequence stratigraphy and 3D seismic data is a sensitive topic in hydrocarbon exploration. Research on subtle traps by geophysical data is the most popular and difficult. Based on the suffi...Forecasting subtle traps by sequence stratigraphy and 3D seismic data is a sensitive topic in hydrocarbon exploration. Research on subtle traps by geophysical data is the most popular and difficult. Based on the sufficiently drilling data, log data, core data and 3D seismic data, sediment sequence of Qikou depression, Huanghua basin was partitioned by using sequence stratigraphy theory. Each sediment sequence system mode was built. Sediment faces of subtle traps were pointed out. Dominating factors forming subtle traps were analyzed. Sandstone seismic rock physics and its response were studied in Tertiary System. Sandstone geophysical response and elastic modulus vary laws with pressure, temperature, porosity, depth were built. Experimental result and practice shows that it is possible using seismic information forecasting subtle traps. Integrated using geology, log, drilling data, special seismic processing technique, interpretation technique, high precision horizon calibration technique, 3D seismic visualizing interpretation, seismic coherence analysis, attribute analysis, logging-constrained inversion, time frequency analysis, subtle trapsobject is identified and interpreted. Finally, advantage object of subtle trap in this area was determined. Bottomland sand stratigraphic and lithologic reservoirs in Qinan slope zone have been founded by means of high resolution 3D seismic data field technique, high resolution 3D seismic data processing technique and seismic wave impendence inversion technique.展开更多
A 1440bp open-reading frame encoding D-hydantoinase from Pseudomonas putida YZ-26 was cloned and sequenced（ GenBank AY387829）. The DNA fragment was inserted into Nde and BamHI sites of vector pET-3a, yielding a reco...A 1440bp open-reading frame encoding D-hydantoinase from Pseudomonas putida YZ-26 was cloned and sequenced（ GenBank AY387829）. The DNA fragment was inserted into Nde and BamHI sites of vector pET-3a, yielding a recombinant plasmid, pET-HDT. After being transferred into the host strain, the artificial strain, pET-HDT/ E. coli BL21 can express the D-hydantoinase as the soluble form in the Lura-Bertani medium without addition of any inducers. The activity of the enzyme toward substrate DL-hydantoin can reach 3000-4000 IU per cells from one-liter bacterial culture incubated at 30 ℃ for 10-12 h. By the comparison of amino acid sequence homology, hydrophobic residues analysis and secondary structure prediction, it was found that D-hydantoinase reported herein is quite similar to that from Pseudomonas putdia CCRC12857, and alike to that from Pseudomonas putdia DSM84 or other bacteria. A rapid and efficient purification procedure of the enzyme was performed by a three-step procedure： ammonium sulfate fractionation, phenyl Sepharose hydrophobic interaction chromatography and Sephacryl S-200 gel filtration. The molecular mass of the monomeric enzyme is 52042 Da as determined by MALDI-TOF mass spectrometry.展开更多
Stream cipher, DNA cryptography and DNA analysis are the most important R&D fields in both Cryptography and Bioinformatics. HC-256 is an emerged scheme as the new generation of stream ciphers for advanced network ...Stream cipher, DNA cryptography and DNA analysis are the most important R&D fields in both Cryptography and Bioinformatics. HC-256 is an emerged scheme as the new generation of stream ciphers for advanced network security. From a random sequencing viewpoint, both sequences of HC-256 and real DNA data may have intrinsic pseudo-random properties respectively. In a recent decade, many DNA sequencing projects are developed on cells, plants and animals over the world into huge DNA databases. Researchers notice that mammalian genomes encode thousands of large noncoding RNAs (lncRNAs), interact with chromatin regulatory complexes, and are thought to play a role in localizing these complexes to target loci across the genome. It is a challenge target using higher dimensional visualization tools to organize various complex interactive properties as visual maps. The Variant Map System (VMS) as an emerging scheme is systematically proposed in this paper to apply multiple maps that used four Meta symbols as same as DNA or RNA representations. System architecture of key components and core mechanism on the VMS are described. Key modules, equations and their I/O parameters are discussed. Applying the VM System, two sets of real DNA sequences from both sample human (noncoding DNA) and corn (coding DNA) genomes are collected in comparison with pseudo DNA sequences generated by HC-256 to show their intrinsic properties in higher levels of similar relationships among relevant DNA sequences on 2D maps. Sample 2D maps are listed and their characteristics are illustrated under controllable environment. Visual results are briefly analyzed to explore their intrinsic properties on selected genome sequences.展开更多
By means of PCR,the gene encoding gD of bovine herpesvirus-1 (BHV-1) strain Luojing was amplified,cloned and sequenced.The nucleotide sequence of this gD gene was (1 251 bp,)encoding 417 amino acids.Comparied with the...By means of PCR,the gene encoding gD of bovine herpesvirus-1 (BHV-1) strain Luojing was amplified,cloned and sequenced.The nucleotide sequence of this gD gene was (1 251 bp,)encoding 417 amino acids.Comparied with the published P8-2 strain,the homology of the necleotide sequence is 99.92%,and that of the deduced amino acid sequence is 100%.The results indicated that gD of BHV-1 was highly conservative.展开更多
Using the complete genome of Plasmodium falciparum 3D7 which has 14 chromosomes as an example, we have examined the distribution functions for the amount of C or G and A or T consecutively and non-overlapping blocks o...Using the complete genome of Plasmodium falciparum 3D7 which has 14 chromosomes as an example, we have examined the distribution functions for the amount of C or G and A or T consecutively and non-overlapping blocks of m bases in this system. The function P(S) about the number of the consecutive C-G or A-T content cluster conforms to the relation P(S)∝e? ; αs values of the scaling exponent αCG are much larger than αAT; and αAT of 14 chromosomes are hardly changed, whereas αCG of 14 chromosomes have a number of fluctuations. We found maximum value of A-T cluster size is much larger than C-G, which implies the existence of large A-T cluster. Our study of the width function ξ(m) of cluster C-G content showed that follows good power law ξ(m)∝m?γ. The average γ for 14 chromosomes is 0.931. These investigations provide some insight into the nucleotide clusters of DNA sequences, and help us understand other properties of DNA sequences.展开更多
In this paper,an innovative 3D motion parameters estimation method from stereo image sequences based on infrared(IR) reflective markers is presented.It was assumed that two high speed CCD cameras had been calibrated p...In this paper,an innovative 3D motion parameters estimation method from stereo image sequences based on infrared(IR) reflective markers is presented.It was assumed that two high speed CCD cameras had been calibrated previously.The method consists of the following steps:1) the coordinate of several markers and depth map for each stereo pair was determined from the sequences of stereo images by relations of markers' coordinate the correspondence between markers was established,2) the 3D motion parameters of the target was computed based upon the matched markers' coordinate,and 3) translated 3D motion parameters estimation into the problem of least square according to the movement model of the object to be measured.Without using line,curve or corner correspondence,this method can calculate the depth of these markers feature easily and quickly in contrast to traditional approaches.The two CCD cameras work on 200 f/s,and each processing cost time is about 3 ms.It was found that,by using several markers and a large number of stereo images,this method can improve the computational speed,robustness and numerical accuracy of the motion parameters in comparison with traditional methods.The virtual simulation experiment was conducted using synthesized stereo image sequences based on 6-DOF motion platform and the experimental results proved the validity of our approach and showed that the translation and rotation precision is up to 0.1 mm and 0.1°.展开更多
The use of sequential stratigraphy concept, based on well logs, sedimentology, and biostratigraphy, has shed light on the complex mechanisms controlling sedimentary accumulations. Consequently, identifying these mecha...The use of sequential stratigraphy concept, based on well logs, sedimentology, and biostratigraphy, has shed light on the complex mechanisms controlling sedimentary accumulations. Consequently, identifying these mechanisms allows us to predict the hydrocarbon generation potential of source rocks. In the Ivorian offshore sedimentary basin, certain studies have contributed to understanding and characterizing the petroleum system. However, these previous works did not integrate biostratigraphic data to highlight sedimentary facies. This study, conducted on two wells in the Abidjan margin, is crucial as it helps us comprehend the geometry of fossil sediments in relation to sea level variations. It will also aid in reconstructing the basin-filling history and predicting the distribution of rocks capable of trapping oil, determining lowstand systems tracts (reservoir rocks), transgressive systems tracts, and highstand systems tracts (cap rocks). Lithological analysis revealed predominantly clayey sedimentation with sandy layers. Well log data facilitated the delineation of formation boundaries and highlighted reservoirs consisting of sands, sandstones, limestones, and occasionally intercalated shales. Integrating these analysis results with biostratigraphic interpretations based on foraminifera and palynomorphs revealed that the traversed formations were deposited in a transitional environment ranging from Coniacian to Maastrichtian ages. Applying sequential stratigraphy concept from well logging resolved dating issues encountered in microfossil-poor or microfossil-free zones. The results of the Coniacian-Maastrichtian age sequential subdivision were aligned with the chart.展开更多
基金Project supported by the National Natural Science Foundation of China (Grant No 60575038)the Natural Science Foundation of Jiangnan University,China (Grant No 20070365)
文摘Chaos game representation （CGR） is an iterative mapping technique that processes sequences of units, such as nucleotides in a DNA sequence or amino acids in a protein, in order to determine the coordinates of their positions in a continuous space. This distribution of positions has two features： one is unique, and the other is source sequence that can be recovered from the coordinates so that the distance between positions may serve as a measure of similarity between the corresponding sequences. A CGR-walk model is proposed based on CGR coordinates for the DNA sequences. The CGR coordinates are converted into a time series, and a long-memory ARFIMA （p, d, q） model, where ARFIMA stands for autoregressive fractionally integrated moving average, is introduced into the DNA sequence analysis. This model is applied to simulating real CGR-walk sequence data of ten genomic sequences. Remarkably long-range correlations are uncovered in the data, and the results from these models are reasonably fitted with those from the ARFIMA （p, d, q） model.
基金Project supported by the National Natural Science Foundation of China (Grant No 60575038)the Natural Science Foundation of Jiangnan University, China (Grant No 20070365)the Program for Innovative Research Team of Jiangnan University, China
文摘A new chaos game representation of protein sequences based on the detailed hydrophobic-hydrophilic （HP） model has been proposed by Yu et al （Physica A 337（2004） 171）. A CGR-walk model is proposed based on the new CGR coordinates for the protein sequences from complete genomes in the present paper. The new CCR coordinates based on the detailed HP model are converted into a time series, and a long-memory ARFIMA（p, d, q） model is introduced into the protein sequence analysis. This model is applied to simulating real CCR-walk sequence data of twelve protein sequences. Remarkably long-range correlations are uncovered in the data and the results obtained from these models are reasonably consistent with those available from the ARFIMA（p, d, q） model.
文摘An effective approach, mapping the texture for building model based on the digital photogrammetric theory, is proposed. The easily-acquired image sequences from digital video camera on helicopter are used as texture resource, and the correspondence between the space edge in building geometry model and its line feature in image sequences is determined semi-automatically. The experimental results in production of three-dimensional data for car navigation show us an attractive future both in efficiency and effect.
基金Project(2003034470) supported by the Postdoctoral Science Foundation of China project supported by the Postdoctoral Science Foundation of Central South University
文摘Forecasting subtle traps by sequence stratigraphy and 3D seismic data is a sensitive topic in hydrocarbon exploration. Research on subtle traps by geophysical data is the most popular and difficult. Based on the sufficiently drilling data, log data, core data and 3D seismic data, sediment sequence of Qikou depression, Huanghua basin was partitioned by using sequence stratigraphy theory. Each sediment sequence system mode was built. Sediment faces of subtle traps were pointed out. Dominating factors forming subtle traps were analyzed. Sandstone seismic rock physics and its response were studied in Tertiary System. Sandstone geophysical response and elastic modulus vary laws with pressure, temperature, porosity, depth were built. Experimental result and practice shows that it is possible using seismic information forecasting subtle traps. Integrated using geology, log, drilling data, special seismic processing technique, interpretation technique, high precision horizon calibration technique, 3D seismic visualizing interpretation, seismic coherence analysis, attribute analysis, logging-constrained inversion, time frequency analysis, subtle trapsobject is identified and interpreted. Finally, advantage object of subtle trap in this area was determined. Bottomland sand stratigraphic and lithologic reservoirs in Qinan slope zone have been founded by means of high resolution 3D seismic data field technique, high resolution 3D seismic data processing technique and seismic wave impendence inversion technique.
基金Supported by the Natural Science Foundation of Shanxi Province(No.20031042).
文摘A 1440bp open-reading frame encoding D-hydantoinase from Pseudomonas putida YZ-26 was cloned and sequenced（ GenBank AY387829）. The DNA fragment was inserted into Nde and BamHI sites of vector pET-3a, yielding a recombinant plasmid, pET-HDT. After being transferred into the host strain, the artificial strain, pET-HDT/ E. coli BL21 can express the D-hydantoinase as the soluble form in the Lura-Bertani medium without addition of any inducers. The activity of the enzyme toward substrate DL-hydantoin can reach 3000-4000 IU per cells from one-liter bacterial culture incubated at 30 ℃ for 10-12 h. By the comparison of amino acid sequence homology, hydrophobic residues analysis and secondary structure prediction, it was found that D-hydantoinase reported herein is quite similar to that from Pseudomonas putdia CCRC12857, and alike to that from Pseudomonas putdia DSM84 or other bacteria. A rapid and efficient purification procedure of the enzyme was performed by a three-step procedure： ammonium sulfate fractionation, phenyl Sepharose hydrophobic interaction chromatography and Sephacryl S-200 gel filtration. The molecular mass of the monomeric enzyme is 52042 Da as determined by MALDI-TOF mass spectrometry.
文摘Stream cipher, DNA cryptography and DNA analysis are the most important R&D fields in both Cryptography and Bioinformatics. HC-256 is an emerged scheme as the new generation of stream ciphers for advanced network security. From a random sequencing viewpoint, both sequences of HC-256 and real DNA data may have intrinsic pseudo-random properties respectively. In a recent decade, many DNA sequencing projects are developed on cells, plants and animals over the world into huge DNA databases. Researchers notice that mammalian genomes encode thousands of large noncoding RNAs (lncRNAs), interact with chromatin regulatory complexes, and are thought to play a role in localizing these complexes to target loci across the genome. It is a challenge target using higher dimensional visualization tools to organize various complex interactive properties as visual maps. The Variant Map System (VMS) as an emerging scheme is systematically proposed in this paper to apply multiple maps that used four Meta symbols as same as DNA or RNA representations. System architecture of key components and core mechanism on the VMS are described. Key modules, equations and their I/O parameters are discussed. Applying the VM System, two sets of real DNA sequences from both sample human (noncoding DNA) and corn (coding DNA) genomes are collected in comparison with pseudo DNA sequences generated by HC-256 to show their intrinsic properties in higher levels of similar relationships among relevant DNA sequences on 2D maps. Sample 2D maps are listed and their characteristics are illustrated under controllable environment. Visual results are briefly analyzed to explore their intrinsic properties on selected genome sequences.
文摘By means of PCR,the gene encoding gD of bovine herpesvirus-1 (BHV-1) strain Luojing was amplified,cloned and sequenced.The nucleotide sequence of this gD gene was (1 251 bp,)encoding 417 amino acids.Comparied with the published P8-2 strain,the homology of the necleotide sequence is 99.92%,and that of the deduced amino acid sequence is 100%.The results indicated that gD of BHV-1 was highly conservative.
基金Project supported by the National Natural Science Foundation ofChina (Nos. 20174036 20274040)+2 种基金 and the Natural Science Founda-tion of Zhejiang Province (Nos. R404047 10102) China
文摘Using the complete genome of Plasmodium falciparum 3D7 which has 14 chromosomes as an example, we have examined the distribution functions for the amount of C or G and A or T consecutively and non-overlapping blocks of m bases in this system. The function P(S) about the number of the consecutive C-G or A-T content cluster conforms to the relation P(S)∝e? ; αs values of the scaling exponent αCG are much larger than αAT; and αAT of 14 chromosomes are hardly changed, whereas αCG of 14 chromosomes have a number of fluctuations. We found maximum value of A-T cluster size is much larger than C-G, which implies the existence of large A-T cluster. Our study of the width function ξ(m) of cluster C-G content showed that follows good power law ξ(m)∝m?γ. The average γ for 14 chromosomes is 0.931. These investigations provide some insight into the nucleotide clusters of DNA sequences, and help us understand other properties of DNA sequences.
基金Sponsored by the National Natural Science Foundation of China(Grant No. 50275040)
文摘In this paper,an innovative 3D motion parameters estimation method from stereo image sequences based on infrared(IR) reflective markers is presented.It was assumed that two high speed CCD cameras had been calibrated previously.The method consists of the following steps:1) the coordinate of several markers and depth map for each stereo pair was determined from the sequences of stereo images by relations of markers' coordinate the correspondence between markers was established,2) the 3D motion parameters of the target was computed based upon the matched markers' coordinate,and 3) translated 3D motion parameters estimation into the problem of least square according to the movement model of the object to be measured.Without using line,curve or corner correspondence,this method can calculate the depth of these markers feature easily and quickly in contrast to traditional approaches.The two CCD cameras work on 200 f/s,and each processing cost time is about 3 ms.It was found that,by using several markers and a large number of stereo images,this method can improve the computational speed,robustness and numerical accuracy of the motion parameters in comparison with traditional methods.The virtual simulation experiment was conducted using synthesized stereo image sequences based on 6-DOF motion platform and the experimental results proved the validity of our approach and showed that the translation and rotation precision is up to 0.1 mm and 0.1°.
文摘The use of sequential stratigraphy concept, based on well logs, sedimentology, and biostratigraphy, has shed light on the complex mechanisms controlling sedimentary accumulations. Consequently, identifying these mechanisms allows us to predict the hydrocarbon generation potential of source rocks. In the Ivorian offshore sedimentary basin, certain studies have contributed to understanding and characterizing the petroleum system. However, these previous works did not integrate biostratigraphic data to highlight sedimentary facies. This study, conducted on two wells in the Abidjan margin, is crucial as it helps us comprehend the geometry of fossil sediments in relation to sea level variations. It will also aid in reconstructing the basin-filling history and predicting the distribution of rocks capable of trapping oil, determining lowstand systems tracts (reservoir rocks), transgressive systems tracts, and highstand systems tracts (cap rocks). Lithological analysis revealed predominantly clayey sedimentation with sandy layers. Well log data facilitated the delineation of formation boundaries and highlighted reservoirs consisting of sands, sandstones, limestones, and occasionally intercalated shales. Integrating these analysis results with biostratigraphic interpretations based on foraminifera and palynomorphs revealed that the traversed formations were deposited in a transitional environment ranging from Coniacian to Maastrichtian ages. Applying sequential stratigraphy concept from well logging resolved dating issues encountered in microfossil-poor or microfossil-free zones. The results of the Coniacian-Maastrichtian age sequential subdivision were aligned with the chart.
