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Multiple Sequence Alignment of the M Protein in SARS-Associated and Other Known Coronaviruses 认领 引用 被引量：1
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作者 史定华 周晖杰 +2 位作者 王斌宾 顾燕红 王翼飞 《Journal of Shanghai University(English Edition)》 2003年第2期118-123,共6页
In this paper, we report a multiple sequence alignment result on the basis of 10 amino acid sequences of the M protein, which come from different coronaviruses (4 SARS associated and 6 others known). The alignment mod... In this paper, we report a multiple sequence alignment result on the basis of 10 amino acid sequences of the M protein, which come from different coronaviruses (4 SARS associated and 6 others known). The alignment model was based on the profile HMM (Hidden Markov Model), and the model training was implemented through the SAHMM (Self Adapting Hidden Markov Model) software developed by the authors. 展开更多
关键词 SARS (Severe Acute Respiratory Syndrome) coronavirus M (Membrane or Matrix) protein multiple sequence alignment profile HMM.
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VCSRA:A fast and accurate multiple sequence alignment algorithm with a high degree of parallelism 认领 引用
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作者 Dong Dong Wenhe Su +2 位作者 Wenqiang Shi Quan Zou Shaoliang Peng 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2018年第7期407-410,共4页
Multiple sequence alignment （MSA） is the alignment among more than two molecular biological sequences, which is a fundamental method to analyze evolutionary events such as mutations, insertions, deletions, and re-ar... Multiple sequence alignment （MSA） is the alignment among more than two molecular biological sequences, which is a fundamental method to analyze evolutionary events such as mutations, insertions, deletions, and re-arrangements. In theory, a dynamic programming algorithm can be employed to produce the optimal MSA. However, this leads to an explosive increase in computing time and memory consumption as the number of sequences increases （Taylor, 1990）. So far, MSA is still regarded as one of the most challenging problems in bioinformatics and computational biology （Chatzou et al., 2016）. 展开更多
关键词 VCSRA A fast and accurate multiple sequence alignment algorithm a high degree of parallelism
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Similarity Measurement of Web Sessions Based on Sequence Alignment 认领 引用
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作者 LI Chaofeng LU Yansheng 《Wuhan University Journal of Natural Sciences》 CAS 2007年第5期814-818,共5页
The task of clustering Web sessions is to group Web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-group similarity. The first and foremost question neede... The task of clustering Web sessions is to group Web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-group similarity. The first and foremost question needed to be considered in clustering Web sessions is how to measure the similarity between Web sessions. However, there are many shortcomings in traditional measurements. This paper introduces a new method for measuring similarities between Web pages that takes into account not only the URL but also the viewing time of the visited Web page. Then we give a new method to measure the similarity of Web sessions using sequence alignment and the similarity of Web page access in detail Experiments have proved that our method is valid and efficient. 展开更多
关键词 Web usage mining clustering Web session sequence alignment
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A Complete and Accurate Short Sequence Alignment Algorithm for Repeats 认领 引用
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作者 Shuaibin Lian Tianliang Liu +2 位作者 Ke Gong Xinwu Chen Gang Zheng 《Journal of Biosciences and Medicines》 2016年第12期144-151,共8页
Eukaryotic genomes contain a significant fraction of repeats, which have very important biomedical function. Thus, aligning repeats from short sequences back to reference genome is the key step for further genome anal... Eukaryotic genomes contain a significant fraction of repeats, which have very important biomedical function. Thus, aligning repeats from short sequences back to reference genome is the key step for further genome analysis. Unfortunately, the current aligning algorithms performed poorly in distinguishing repeats and nonrepeats. To this end, we proposed a new algorithm, named HashRepAligner, to address this problem. Finally, the cross comparison with other algorithms was performed, and the results indicated that HashRepAligner outperformed other aligners in terms of the detecting repeats. 展开更多
关键词 Sequence Alignment Next Generation Sequencing Hash Index Repeats Detection
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GPU acceleration for DNA sequence alignment algorithm and its application 认领 引用
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作者 Heming Zhong Xiaojian Pan +3 位作者 Zengquang He Haoling Wang Dan Huang Zhiguang Chen 《CCF Transactions on High Performance Computing》 EI CSCD 2025年第2期169-177,共9页
With the rapid development of Next-Generation Sequencing(NGS)technology,genome sequencing services for clinical fields are now bringing new challenges to existing solutions.The increasing demand for alignment data pro... With the rapid development of Next-Generation Sequencing(NGS)technology,genome sequencing services for clinical fields are now bringing new challenges to existing solutions.The increasing demand for alignment data processing motivates the development of more efficient algorithms for computational genomics.The Pair-Hidden Markov Model(Pair-HMM)is one of the most popular models used to process sequence alignment.Its related Forward Algorithm(FA)is usually the key performance bottleneck of the entire variant calling workflow.While multiple previous works have been conducted in efforts to accelerate the algorithm with various levels of parallelization,it still lacks of fully utilizing the resources of heterogeneous devices,such as high-bandwidth memory and massive SIMD cores in advanced GPU.In this paper,we design a GPU-based Pari-HMM sequence alignment algorithm and conduct its implementation with holistic co-design optimizations,including efficient computational parallelization,parameter initialization,memory accessing layout,and etc.When using Nvidia Telsa V100 GPU,Our work has shown speedups of 1151x compared to the Java baseline on Intel single-core CPU and 1.47x to the previous state-of-art GPU work. 展开更多
关键词 High performance computing GPU acceleration DNA sequence alignment CUDA implementation Pair-HMM
Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment 认领 引用 被引量：2
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作者 谭光明 徐琳 +2 位作者 卜东波 冯圣中 孙凝晖 《Journal of Computer Science & Technology》 SCIE EI 2006年第6期973-978,共6页
MegaBlast is one of the most important programs in NCBI BLAST （Basic Local Alignment Search Tool） toolkits, tIowever, MegaBlast is computation and I/O intensive. It consumes a great deal of memory which is proportio... MegaBlast is one of the most important programs in NCBI BLAST （Basic Local Alignment Search Tool） toolkits, tIowever, MegaBlast is computation and I/O intensive. It consumes a great deal of memory which is proportional to the size of the query sequences set and subject （database） sequences set of product. This paper proposes a new strategy for optimizing MegaBlast. The new strategy exchanges the query and subject sequences sets, and builds a hash table based on new subject sequences. It overlaps I/O with computation, shortens the overall time and reduces the cost of memory, since the memory here is only proportional to the size of subject sequences set. The optimized algorithm is suitable to be parallelized in cluster systems. The parallel algorithm uses query segmentation method. As our experiments shown, the parallel program which is implemented with MPI has fine scalability. 展开更多
关键词 sequence alignment BLAST MegaBlast I/O intensive parallelization
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Artificial Fish Swarm for Multi Protein Sequences Alignment in Bioinformatics 认领 引用
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作者 Medhat A.Tawfeek Saad Alanazi A.A.Abd El-Aziz 《Computers, Materials & Continua》 SCIE EI 2022年第9期6091-6106,共16页
The alignment operation between many protein sequences or DNAsequences related to the scientific bioinformatics application is very complex.There is a trade-off in the objectives in the existing techniques of Multiple... The alignment operation between many protein sequences or DNAsequences related to the scientific bioinformatics application is very complex.There is a trade-off in the objectives in the existing techniques of MultipleSequence Alignment (MSA). The techniques that concern with speed ignoreaccuracy, whereas techniques that concern with accuracy ignore speed. Theterm alignment means to get the similarity in different sequences with highaccuracy. The more growing number of sequences leads to a very complexand complicated problem. Because of the emergence;rapid development;anddependence on gene sequencing, sequence alignment has become importantin every biological relationship analysis process. Calculating the numberof similar amino acids is the primary method for proving that there is arelationship between two sequences. The time is a main issue in any alignmenttechnique. In this paper, a more effective MSA method for handling themassive multiple protein sequences alignment maintaining the highest accuracy with less time consumption is proposed. The proposed method dependson Artificial Fish Swarm (AFS) algorithm that can break down the mostchallenges of MSA problems. The AFS is exploited to obtain high accuracyin adequate time. ASF has been increasing popularly in various applicationssuch as artificial intelligence, computer vision, machine learning, and dataintensive application. It basically mimics the behavior of fish trying to getthe food in nature. The proposed mechanisms of AFS that is like preying,swarming, following, moving, and leaping help in increasing the accuracy andconcerning the speed by decreasing execution time. The sense organs that aidthe artificial fishes to collect information and vision from the environmenthelp in concerning the accuracy. These features of the proposed AFS make thealignment operation more efficient and are suitable especially for large-scaledata. The implementation and experimental results put the proposed AFS as afirst choice in the queue of alignment compared to the well-known algorithmsin multiple sequence alignment. 展开更多
关键词 Multiple sequence alignment swarm intelligence artificial fish swarm protein sequences
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Fast vectorized distance matrix computation for multiple sequence alignment on multi-cores 认领 引用
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作者 Mohammed W. A1-Neama Naglaa M. Reda Fayed F. M. Ghaleb 《International Journal of Biomathematics》 SCIE 2015年第6期243-257,共15页
Although high quality multiple sequence alignment is an essential task in bioinforma- tics, it becomes a big dilemma nowadays due to the gigantic explosion in the amount of molecular data. The most consuming time and ... Although high quality multiple sequence alignment is an essential task in bioinforma- tics, it becomes a big dilemma nowadays due to the gigantic explosion in the amount of molecular data. The most consuming time and space phase is the distance matrix computation. This paper addresses this issue by proposing a vectorized parallel method that accomplishes the huge number of similarity comparisons faster in less space. Per- formance tests on real biological datasets using core-iT show superior results in terms of time and space. 展开更多
关键词 Bioinformatics multiple sequence alignment distance matrix parallel programming multi-cores.
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On the Edge of Web-Based Multiple Sequence Alignment Services 认领 引用
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作者 Ken D. Nguyen 《Tsinghua Science and Technology》 EI CAS 2012年第6期629-637,共9页
There are many web-based multiple sequence alignment services accessible around the world. However, many researchers working on biological sequence analysis still struggle with inefficient, unfriendly user interface, ... There are many web-based multiple sequence alignment services accessible around the world. However, many researchers working on biological sequence analysis still struggle with inefficient, unfriendly user interface, and limited capability multiple sequence alignment software. In this study, we provide a comprehensive survey of regional and continental facilities that provide web-based alignment services. We also analyze and identify much needed services that are not available through these existing service providers. We then implement a web-based model to address these needs. From that perspective, our web-based multiple sequence alignment server, SeqAna, provides a unique set of services that none of these studied facilities have. For example, SeqAna provides a multiple sequence alignment scoring and ranking service. This service, the only of its kind, allows SeqAna＇s users to perform multiple sequence alignment with several alignment tools and rank the results of these alignments in the order of quality. With this service, SeqAna＇s users will be able to identify which alignment tools are more appropriate for their specific set of sequences. In addition, SeqAna＇s users can customize a small alignment sample as a reference for SeqAna to automatically identify the best tool to align their large set of sequences. 展开更多
关键词 bioinformatics multiple sequence alignment web-services multiple sequence ranking
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Brief Introduction to Self-Adapting Hidden Markov Model Program for Multiple Sequences Alignment 认领 引用 被引量：1
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作者 GuYan－hong SHIDing－hua 《Journal of Shanghai University(English Edition)》 2001年第2期93-95,共3页
In this letter, we briefly describe a program of self adapting hidden Markov model (SA HMM) and its application in multiple sequences alignment. Program consists of two stage optimisation algorithm.
关键词 hidden Markov model (HMM) profile HMM multiple sequences alignment bioinformatics
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Efficient computation of Hash Hirschberg protein alignment utilizing hyper threading multi-core sharing technology 认领 引用 被引量：4
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作者 Muhannad Abu-Hashem Adnan Gutub 《CAAI Transactions on Intelligence Technology》 SCIE EI 2022年第2期278-291,共14页
Due to current technology enhancement,molecular databases have exponentially grown requesting faster efficient methods that can handle these amounts of huge data.There-fore,Multi-processing CPUs technology can be used... Due to current technology enhancement,molecular databases have exponentially grown requesting faster efficient methods that can handle these amounts of huge data.There-fore,Multi-processing CPUs technology can be used including physical and logical processors(Hyper Threading)to significantly increase the performance of computations.Accordingly,sequence comparison and pairwise alignment were both found contributing significantly in calculating the resemblance between sequences for constructing optimal alignments.This research used the Hash Table-NGram-Hirschberg(HT-NGH)algo-rithm to represent this pairwise alignment utilizing hashing capabilities.The authors propose using parallel shared memory architecture via Hyper Threading to improve the performance of molecular dataset protein pairwise alignment.The proposed parallel hyper threading method targeted the transformation of the HT-NGH on the datasets decomposition for sequence level efficient utilization within the processing units,that is,reducing idle processing unit situations.The authors combined hyper threading within the multicore architecture processing on shared memory utilization remarking perfor-mance of 24.8%average speed up to 34.4%as the highest boosting rate.The benefit of this work improvement is shown preserving acceptable accuracy,that is,reaching 2.08,2.88,and 3.87 boost-up as well as the efficiency of 1.04,0.96,and 0.97,using 2,3,and 4 cores,respectively,as attractive remarkable results. 展开更多
关键词 computational biology high-performance computing Hyper Threading pairwise sequence alignment parallel design sequence alignment shared-memory
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Isolation,identification and pathogenicity of two root rot pathogens Fusarium solani in citrus 认领 引用 被引量：1
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作者 Tao Zhu Xuzhao Luo +5 位作者 Chenxing Hao Zhimei Zhu Lian Liu Ziniu Deng Yunlin Cao Xianfeng Ma 《Horticultural Plant Journal》 SCIE CAS CSCD 2026年第1期127-135,共9页
Root rot is a prevalent soil-borne fungal disease in citrus.Citron C-05(Citrus medica)stands out as a germplasm within Citrus spp.due to its complete resistance to citrus canker and favorable characteristics such as s... Root rot is a prevalent soil-borne fungal disease in citrus.Citron C-05(Citrus medica)stands out as a germplasm within Citrus spp.due to its complete resistance to citrus canker and favorable characteristics such as single embryo and easy rooting.However,Citron C-05 was found to be highly susceptible to root rot during cultivation,with the specific pathogens previously unknown.In this study,four candidate fungal species were isolated from Citron C-05 roots.Sequence analysis of ITS,EF-1a,RPB1,and RPB2 identified two Fusarium solani strains,Rr-2 and Rr-4,as the candidates causing root rot in Citron C-05.Resistance tests showed these two pathogens increased root damage rate from 10.30%to 35.69%in Citron C-05,sour orange(Citrus aurantium),sweet orange(Citrus sinensis)and pummelo(Citrus grandis).F.solani exhibited the weak pathogenicity towards trifoliate orange(Poncirus trifoliata).DAB staining revealed none of reddish-brown precipitation in the four susceptible citrus germplasm after infection with F.solani,while trifoliate orange exhibited significant H2O2 accumulation.Trypan blue staining indicated increased cell death in the four susceptible citrus germplasm following infection with these two pathogens but not in trifoliate orange.These findings provide a comprehensive understanding of citrus root rot and support future research on the mechanisms of root rot resistance in citrus. 展开更多
关键词 Citron C-05 Root rot Fusarium solani Fungal pathogen identification Multiple sequence alignment Pathogenicity
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ORPA:a fast and efficient phylogenetic analysis method for constructing genome-wide alignments of organelle genomes 认领 引用 被引量：2
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作者 Guiqi Bi Xinxin Luan Jianbin Yan 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2024年第3期352-358,共7页
Creating a multi-gene alignment matrix for phylogenetic analysis using organelle genomes involves aligning single-gene datasets manually,a process that can be time-consuming and prone to errors.The HomBlocks pipeline ... Creating a multi-gene alignment matrix for phylogenetic analysis using organelle genomes involves aligning single-gene datasets manually,a process that can be time-consuming and prone to errors.The HomBlocks pipeline has been created to eliminate the inaccuracies arising from manual operations.The processing of a large number of sequences,however,remains a time-consuming task.To conquer this challenge,we develop a speedy and efficient method called Organelle Genomes for Phylogenetic Analysis(ORPA).ORPA can quickly generate multiple sequence alignments for whole-genome comparisons by parsing the result files of NCBI BLAST,completing the task just in 1 min.With increasing data volume,the efficiency of ORPA is even more pronounced,over 300 times faster than HomBlocks in aligning 60 high-plant chloroplast genomes.The phylogenetic tree outputs from ORPA are equivalent to HomBlocks,indicating its outstanding efficiency.Due to its speed and accuracy,ORPA can identify species-level evolutionary conflicts,providing valuable insights into evolutionary cognition. 展开更多
关键词 Ultrafast alignment Organelle phylogenomics Phylogenomic conflict Efficient pipeline Multiple sequence alignment pipeline
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Genetic Diversity of Chinese Soybean mosaic virus Strains and Their Relationships with Other Plant Potyviruses Based on P3 Gene Sequences 认领 引用 被引量：1
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作者 YANG Qing-hua LI Kai +1 位作者 ZHI Hai-jian GAI Jun-yi 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2014年第10期2184-2195,共12页
Soybean mosaic virus （SMV）, a member of the genus Potyvirus, is a major pathogen of soybean plants in China, and 16 SMV strains have been identified nationwide based on a former detailed SMV classification system. A... Soybean mosaic virus （SMV）, a member of the genus Potyvirus, is a major pathogen of soybean plants in China, and 16 SMV strains have been identified nationwide based on a former detailed SMV classification system. As the P3 gene is thought to be involved in viral replication, systemic infection, pathogenicity, and overcoming resistance, knowledge of the P3 gene sequences of SMV and other potyviruses would be useful in efforts to know the genetic relationships among them and control the disease. P3 gene sequences were obtained from representative isolates of the above-mentioned 16 SMV strains and were compared with other SMV strains and 16 Potyvirus species from the National Center for Biotechnology GenBank database. The P3 genes from the 16 SMV isolates are composed of 1041 nucleotides, encoding 347 amino acids, and share 90.7-100% nucleotide （NT） sequence identities and 95.1-100% amino acid （AA） sequence identities. The P3 coding regions of the 16 SMV isolates share high identities （92.4-98.9% NT and 96.0-100% AA） with the reported Korean isolates, followed by the USA isolates （88.5-97.9% NT and 91.4-98.6% AA）, and share low identities （80.5-85.2% NT and 82.1-84.7% AA） with the reported HZ 1 and P isolates from Pinellia ternata. The sequence identities of the P3 genes between SMV and the 16 potyviruses varied from 44.4 to 81.9% in the NT sequences and from 21.4 to 85.3% in the AA sequences, respectively. Among them, SMV was closely related to Watermelon mosaic virus （WMV）, with 76.0-81.9% NT and 77.5-85.3% AA identities. In addition, the SMV isolates and potyvirus species were clustered into six distinct groups. All the SMV strains isolated from soybean were clustered in Group I, and the remaining species were clustered in other groups. A multiple sequence alignment analysis of the C-terminal regions indicated that the P3 genes within a species were highly conserved, whereas those among species were relatively variable. 展开更多
关键词 Soybean mosaic virus Potyvirus P3 gene homology analysis phylogenetic tree multiple sequence alignment
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Modeling Bacterial Species: Using Sequence Similarity with Clustering Techniques 认领 引用
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作者 Miguel-Angel Sicilia Elena García-Barriocanal +2 位作者 Marçal Mora-Cantallops Salvador Sánchez-Alonso Lino González 《Computers, Materials & Continua》 SCIE EI 2021年第8期1661-1672,共12页
Existing studies have challenged the current definition of named bacterial species,especially in the case of highly recombinogenic bacteria.This has led to considering the use of computational procedures to examine po... Existing studies have challenged the current definition of named bacterial species,especially in the case of highly recombinogenic bacteria.This has led to considering the use of computational procedures to examine potential bacterial clusters that are not identified by species naming.This paper describes the use of sequence data obtained from MLST databases as input for a k-means algorithm extended to deal with housekeeping gene sequences as a metric of similarity for the clustering process.An implementation of the k-means algorithm has been developed based on an existing source code implementation,and it has been evaluated against MLST data.Results point out to potential bacterial clusters that are close to more than one different named species and thus may become candidates for alternative classifications accounting for genotypic information.The use of hierarchical clustering with sequence comparison as similarity metric has the potential to find clusters different from named species by using a more informed cluster formation strategy than a conventional nominal variant of the algorithm. 展开更多
关键词 Clustering bacterial species k-means sequence alignment
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Facility Layout Based on Sequence Analysis:Design of Flowshops 认领 引用
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作者 周瑾 吴智铭 《Journal of Shanghai Jiaotong university(Science)》 EI 2009年第6期686-689,共4页
A computer-aided method to design a hybrid layout--tree-shape planar flowlines is presented. In newtype fiowshop layout, the common machines shared by several flowlines could be located together in functional sections... A computer-aided method to design a hybrid layout--tree-shape planar flowlines is presented. In newtype fiowshop layout, the common machines shared by several flowlines could be located together in functional sections. The approach combines traditional cell formation techniques with sequence alignment algorithms. Firstly, a sequence analysis based cell formation procedure is adopted; then the operation sequences for parts are aligned to maximize machines adjacency in hyperedge representations; finally a tree-shape planar flowline will be obtained for each part family. With the help of a sample of operation sequences obtained from industry, this algorithm is illustrated. 展开更多
关键词 workshop layout flowlines sequence analysis sequence alignment algorithm
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New geographic distribution and molecular diversity of Citrus chlorotic dwarf-associated virus in China 认领 引用 被引量：4
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作者 YANG Zhen ZHANG Lan +5 位作者 ZHAO Jin-fa ZHANG Xing-kai WANG Ying LI Tai-sheng ZHANG Wei ZHOU Yan 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2022年第1期293-298,共6页
In 2009, an emerging citrus viral disease caused by Citrus chlorotic dwarf-associated virus(CCDaV) was discovered in Yunnan Province of China. However, the occurrence and spread of CCDaV in other citrus-growing provin... In 2009, an emerging citrus viral disease caused by Citrus chlorotic dwarf-associated virus(CCDaV) was discovered in Yunnan Province of China. However, the occurrence and spread of CCDaV in other citrus-growing provinces in China is unknown to date. To better understand the distribution and molecular diversity of CCDaV in China, a total of 1 772 citrus samples were collected from 11 major citrus-growing provinces and were tested for CCDaV by PCR. Among these, 134 citrus samples from Guangxi, Yunnan and Guangdong were tested positive for CCDaV, demonstrating that the occurrence and spread of CCDaV are increasing in China. The complete genome sequences of 17 CCDaV isolates from different provinces and hosts were sequenced. Comparisons of the whole-genome sequences of the 17 CCDaV isolates as well as the 15 isolates available in GenBank revealed that the sequence identity was about 99–100%, showing that the CCDaV isolates were highly conserved. Phylogenetic studies showed that the 32 CCDaV isolates belonged to four different groups based on geographical origins and host species, and that CCDaV isolates from China and Turkey were clustered into different groups. The results provide important information for clarifying the distribution and genetic diversity of CCDaV in China. 展开更多
关键词 Citrus chlorotic dwarf-associated virus detection sequence alignments phylogenetic tree analysis
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Identification of Genetic Variation in Citrus sinensis from Hunan Based on Start Codon Targeted Polymorphism 认领 引用 被引量：10
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作者 蒋巧巧 龙桂友 +1 位作者 李武文 邓子牛 《Agricultural Science & Technology》 CAS 2011年第11期1594-1599,共6页
[Objective] The aim was to identify genetic variation in Citrus sinensis （sweet orange） germplasm from Hunan Province according to the Start Codon Targeted （SCoT） Polymorphism. [Method] The reaction system for SCo... [Objective] The aim was to identify genetic variation in Citrus sinensis （sweet orange） germplasm from Hunan Province according to the Start Codon Targeted （SCoT） Polymorphism. [Method] The reaction system for SCoT amplification from sweet orange was first optimized, and then the SCoT fragments were amplified from 24 sweet orange cultivars collected in Hunan Province and sequenced for genetic variation analysis. [Result] The optimum reaction system for SCoT markers amplification was 2.0 μl containing 80 ng of template DNA, 0.3 mmol/L dNTPs, 0.2 μmol/L primer, 1.6 mmol/L Mg2＋, 1.6 U of Taq DNA polymerase and 10×PCR buffer. By using this reaction system, the PCR products from the sweet orange cultivars produced clear and reproducible bands at 100-2 000 bp through electrophoresis. The SCoT fragments of the 24 sweet orange cultivars were 1 090-1 091 bp, with the homology of 99.84% and nucleotide deletion and substitution. After being sequenced, the SCoT polymorphisms could distinguish 12 sweet orange cultivars. In addition, the BLAST result showed that part of the SCoT fragments coding region shared high homology with ribosomal protein S3 N superfamily. [Conclusion] This study will provide a theoretical basis for breeding sweet orange cultivars. 展开更多
关键词 Citrus sinensis （L.） Osbeck SCoT Uniform design Sequence alignment
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Hidden Markov Models Incorporating Fuzzy Measures and Integrals for Protein Sequence Identification and Alignment 认领 引用 被引量：6
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作者 Niranjan P. Bidargaddi Madhu Chetty Joarder Kamruzzaman 《Genomics, Proteomics & Bioinformatics》 CAS 2008年第2期98-110,共13页
Profile hidden Markov models （HMMs） based on classical HMMs have been widely applied for protein sequence identification. The formulation of the forward and backward variables in profile HMMs is made under statistic... Profile hidden Markov models （HMMs） based on classical HMMs have been widely applied for protein sequence identification. The formulation of the forward and backward variables in profile HMMs is made under statistical independence assumption of the probability theory. We propose a fuzzy profile HMM to overcome the limitations of that assumption and to achieve an improved alignment for protein sequences belonging to a given family. The proposed model fuzzifies the forward and backward variables by incorporating Sugeno fuzzy measures and Choquet integrals, thus further extends the generalized HMM. Based on the fuzzified forward and backward variables, we propose a fuzzy Baum-Welch parameter estimation algorithm for profiles. The strong correlations and the sequence preference involved in the protein structures make this fuzzy architecture based model as a suitable candidate for building profiles of a given family, since the fuzzy set can handle uncertainties better than classical methods. 展开更多
关键词 fuzzy profile HMM sequence alignment fuzzy measure fuzzy integral
Identification of distant co-evolving residues in antigen 85C from Mycobacterium tuberculosis using statistical coupling analysis of the esterase family proteins 认领 引用 被引量：2
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作者 Veeky Baths Utpal Roy 《Journal of Biomedical Research》 CAS 2011年第3期165-169,共5页
A fundamental goal in cellular signaling is to understand allosteric communication, the process by which sig-nals originating at one site in a protein propagate reliably to affect distant functional sites. The general... A fundamental goal in cellular signaling is to understand allosteric communication, the process by which sig-nals originating at one site in a protein propagate reliably to affect distant functional sites. The general principles of protein structure that underlie this process remain unknown. Statistical coupling analysis （SCA） is a statistical technique that uses evolutionary data of a protein family to measure correlation between distant functional sites and suggests allosteric communication. In proteins, very distant and small interactions between collections of amino acids provide the communication which can be important for signaling process. In this paper, we present the SCA of protein alignment of the esterase family （pfam ID： PF00756） containing the sequence of antigen 85C secreted by Mycobacterium tuberculosis to identify a subset of interacting residues. Clustering analysis of the pairwise correlation highlighted seven important residue positions in the esterase family alignments. These resi-dues were then mapped on the crystal structure of antigen 85C （PDB ID： 1DQZ）. The mapping revealed corre-lation between 3 distant residues （Asp38, Leu123 and Met125） and suggests allosteric communication between them. This information can be used for a new drug against this fatal disease. 展开更多
关键词 antigen 85C Mycobacterium tuberculosis clustering analysis covariance statistical coupling analy-sis esterase family multiple sequence alignments pfam Protein Data Bank.
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