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The base composition of the human genes is correlated with the secondary structures of the encoded proteins

GENE 2002年第1-2期300卷 179-187页

作者： D'Onofrio, G Ghosh, TC Bernardi, G Staz Zool Anton Dohrn Lab Evoluz Mol I-80121 Naples Italy Bose Inst Bioinformat Ctr Kolkata 700054 W Bengal India

The analysis of a non-redundant set of human proteins, for which both the crystallographic structures and the corresponding gene sequences are available. show that bases at third codon position are non-uniformly distributed along the coding sequences. Significant compositional differences are found by comparing the gene regions corresponding to the different secondary structures of the proteins. Inter and intra-structure differences were most pronounced in the GC-richest genes. These results are not compatible with any proposed hypotheses based on a neutral process of formation/maintenance of the high GC(3) levels of the genes localized in the GC-richest isochores of the human genome. (C) 2002 Elsevier Science B.V. All rights reserved.

关键词： base composition human protein coding sequence GC(3) isochore encoded protein

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Angle: A sequencing errors resistant program for predicting protein coding regions in unfinished cDNA

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Journal of Bioinformatics and Computational Biology 2006年第3期4卷 649-664页

作者： Shimizu, Kana Adachi, Jun Muraoka, Yoichi Department of Computer Science Graduate School of Waseda University Shinjuku-ku Tokyo 162-0044 17 301 Kikui-cho Japan The Institute of Statistical Mathematics Minato-ku Tokyo 106-8569 4-6-7 Minami-Azabu Japan Department of Biosystems Science The Graduate University for Advanced Studies Hayama Kanagawa 240-0193 Shonan Village Japan Department of Computer Science Graduate School of Waseda University Shinjuku-ku Tokyo 169-8555 3-4-1 Okubo Japan

In the process of making full-length cDNA, predicting protein coding regions helps both in the preliminary analysis of genes and in any succeeding process. However, unfinished cDNA contains artifacts including many sequencing errors, which hinder the correct evaluation of coding sequences. Especially, predictions of short sequences are difficult because they provide little information for evaluating coding potential. In this paper, we describe ANGLE, a new program for predicting coding sequences in low quality cDNA. To achieve error-tolerant prediction, ANGLE uses a machine-learning approach, which makes better expression of coding sequence maximizing the use of limited information from input sequences. Our method utilizes not only codon usage, but also protein structure information which is difficult to be used for stochastic model-based algorithms, and optimizes limited information from a short segment when deciding coding potential, with the result that predictive accuracy does not depend on the length of an input sequence. The performance of ANGLE is compared with ESTSCAN on four dataset each of them having a different error rate (one frame-shift error or one substitution error per 200-500 nucleotides) and on one dataset which has no error. ANGLE outperforms ESTSCAN by 9.26% in average Matthews's correlation coefficient on short sequence dataset (< 1000 bases). On long sequence dataset, ANGLE achieves comparable performance. © 2006 Imperial College Press.

关键词： AdaBoost cDNA coding sequence EST Sequencing errors

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MUI-free receiver for a shift-orthogonal quasi-synchronous DS-CDMA system based on block spreading in frequency-selective fading 25

MUI-free receiver for a shift-orthogonal quasi-synchronous D...

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IEEE International Conference on Acoustics, Speech, and Signal Processing

作者： Leus, G Moonen, M Katholieke Univ Leuven ESAT B-3001 Heverlee Belgium

ISBN: (纸本)0780362934

In this paper, we consider a shift-orthogonal (a shift-orthogonal set of code sequences is used) quasi-synchronous DS-CDMA system based on block spreading in the presence of frequency-selective fading, For such a system, we can develop a simple receiver that eliminates the multi-user interference (MUI) deterministically, without using any channel information, and suppresses the remaining (single-user) inter symbol interference (ISI), using a single-user channel estimation method (training-based or blind) or using a single-user direct approach (training-based or blind). The proposed transceiver is less complex than the recently developed VL-AMOUR transceiver (which has the same properties as the proposed transceiver), while their performances are comparable.

关键词： selective fading CDMA mobile communications quasi-synchronous single user Direct-sequence code-division multiple access Transceivers information channels fading color Receivers coding sequence

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A New Way to Find Similarity/Dissimilarity of DNA sequences on the Basis of Dinucleotides Representation 1

A New Way to Find Similarity/Dissimilarity of DNA Sequences ...

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1st International Conference on Computational Advancement in Communication Circuits and Systems (ICCACCS)

作者： Das, Subhram Palit, Subhra Mahalanabish, Anindya Raj Choudhury, Nobhonil Roy Narula Inst Technol Dept Comp Sci & Engn Kolkata India

ISBN: (纸本)9788132222743;9788132222736

In this paper, we have introduced a new way of representation of dinucleotides. They are directly represented by two-dimensional coordinates (x, y) in the Euclidean plane. By writing z = x x y, ultimately the representation is given by three-dimensional coordinates (x, y, z). Based on the variances of cumulative values x', y', z' of x, y, and z respectively, a measure is determined to compare coding sequences of beta-globin genes of 11 species. We have also used another measure for similar comparison of sequences. This is based on the probability distribution of dinucleotides occurring in the sequence. Finally, we have compared the similarity/dissimilarity matrix obtained under above two measures by the method of correlation coefficient.

关键词： Dinucleotide Graphical representation coding sequence Similarity/dissimilarity analysis Correlation coefficient

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Integrated coding Metasurface in a Single-Layered Printed Circuit Board 21

Integrated Coding Metasurface in a Single-Layered Printed Ci...

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21st International Conference on Electromagnetics in Advanced Applications (ICEAA)

作者： Shen, Yizhu Yang, Jiawei Dou, Wenbin Hu, Sanming Southeast Univ Sch Informat Sci & Engn State Key Lab Millimeter Waves Nanjing Peoples R China

ISBN: (纸本)9781728105635

coding metasurface is a good candidate to achieve flexible electromagnetic wave beam manipulations, but with challenges of integration and alignment issues, especially at millimeter-wave band. To alleviate the above problems, an integrated coding metasurface is designed, to inherently integrate a planar feeding with coding metasurface in a single-layered printed circuit board. In addition, by pre-designing the coding sequence, multiple beam functions can be achieved. As a validation, this paper demonstrates a single coding metasurface to generate boresight pencil beam in the far-field and tilted zero-order Bessel beam in the near-field simultaneously.

关键词： coding metasurface coding pattern coding sequence integrated single-layered

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De novo assembly of leaf transcriptome, functional annotation and genomic resources development in Prosopis cineraria, a multipurpose tree of Indian Thar Desert

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Plant Gene 2017年 12卷 88-97页

作者： Rai, Manoj K. Shekhawat, Jatan K. Kataria, Vinod Shekhawat, N.S. Biotechnology Unit Department of Botany Jai Narain Vyas University Jodhpur 342001 Rajasthan India Department of Environmental Science Indira Gandhi National Tribal University Amarkantak 484887 M.P. India

Prosopis cineraria (L.) Druce, which belongs to the family Fabaceae, is a key component and one of the most valued trees of the Indian Thar Desert. The genetic improvement of P. cineraria has been hindered owing to very limited availability of genomic or transcriptomic resources. In this study, we present first transcriptome analysis of P. cineraria using RNA-Seq technology. The sequencing output of leaf transcriptome generated > 10 million high quality sequence reads, which assembled de novo in 1,42,711 unigenes. A total 60,583 CDS were predicted from unigenes with maximum and mean CDS length of 15,279 and 904 bp, respectively. Based on the similarity searches against plant non-redundant protein database, 57,249 CDS were annotated. The top-hit species distribution revealed that highest similarity was found to be against the species Glycine max (15,372). Based on sequence homology, 24,424 CDS were assigned GO terms. A total of 18,901 (31%) CDS were annotated with biological process, 12,930 (21%) with cellular components and 19,756 (32%) with molecular function. Annotation of transcripts using KEGG database revealed that 7945 CDSs were enriched in 33 different functional pathway categories including five major pathways i.e. metabolism, genetic information processing, environmental information processing, cellular process and organismal systems. The expression of CDSs ranged from 0 to 41,295.83 RPKM, while 950 CDSs had a high expression level of > 100 RPKM. Transcription factor analysis showed 12,128 unique transcripts belonging to the 79 transcription factor families. In addition, a total of 15,878 SSRs were identified in 13,655 unigenes. The transcriptome data set reported in the current study will serve as an important public information platform for comparative and functional genomic as well as gene expression studies in P. cineraria and other closely related species. © 2017 Elsevier B.V.

关键词： coding sequence Functional annotation Gene ontology RNA-Seq Simple sequence repeat Transcription factor

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OPTIMAL coding PATTERN FOR DSSS coding WITH INTERFERENCE MINIMIZATION

OPTIMAL CODING PATTERN FOR DSSS CODING WITH INTERFERENCE MIN...

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IEEE International Conference on Inventive Computation Technologies (ICICT)

作者： Reddy, D. Karunakar Savithri, T. Satya JNTUH Coll Engn Hyderabad Telangana India

Direct sequence spread spectrum (DSSS) is an optimal mode of coding for data communication. Spread spectrum coding were used in various communication modes, which gives an advantage of channel interference minimization, with maximum spectrum utilization. With the simplicity in coding efficiency, this coding approach was most effectively used in various application of data exchange. However, with the increase in code sequence and a random pattern generation limits it significance in usage. To optimize the coding efficiency, a inter correlative coding approach with pseudo random sequence optimization is proposed. The proposed approach has a significance of maximizing multi access interference minimization with lower coding overhead over the conventional coding approach.

关键词： coding sequence inter correlative coding pseudo random sequence optimization direct sequence spread spectrum

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Characterization of the Promoter Region for the EVI2A Gene

Characterization of the Promoter Region for the EVI2A Gene

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作者： Weinstein, Max California State University Northridge

学位级别：硕士

Evolution is driven by natural selection operating on the genes present in a given species. However, it is unclear if the different parts of a gene (coding and non-coding) are under the same types of selection as each other. Determining the similarity of selection between coding and non-coding regions of a gene can be determined using bioinformatics; by analyzing the differences in conserved sites in the coding and non-coding (promoter) regions of the gene. Ecotropic Viral Integration Site 2A was analyzed at both its putative promoter region and its coding DNA sequence to determine its similarity of selection. After identifying the putative promoter region of the EVI2A gene through tracking of conserved regions, the genetic sequences for the EVI2A putative promoter and coding sequences were compared across several different vertebrate species to generate genetic phylogenies, which were then compared against each other and known evolutionary phylogenetic trees. Conserved sequences were identified in both the putative promoter regions and the coding sequences. The motifs conserved in the coding sequence were much more stringently conserved than were the conserved sequences in the putative promoter region, suggesting that the two regions of the EVI2A gene are under different types of selective pressure.

关键词： biology gene regulation evi2a ecotropic viral integration site 2a bioinformatics phylogenetics promoter coding sequence protein motifs transcription factor binding sites

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Využití numerických reprezentací ve zpracování nukleotidových sekvencí

Využití numerických reprezentací ve zpracování nukleot...

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作者： Košíček, Adam Brno University of Technology

Převod sekvencí DNA na vhodnou reprezentaci je důležitou úkolem před samotným započetím analýzy a dalšího zpracování. Hlavním úkolem této práce bylo se sezn&... 详细信息

Převod sekvencí DNA na vhodnou reprezentaci je důležitou úkolem před samotným započetím analýzy a dalšího zpracování. Hlavním úkolem této práce bylo se seznámit s typy numerických a grafických reprezentací a jejich využitím pro analýzu DNA. Vzhledem k velkému množství metod a postupů, byly do této práce vybrány pouze některé. Některé metody nelze přímo klasifikovat jako numerické nebo grafické, protože obsahují možnost obojí reprezentace. Tyto metody byly zařazeny mezi grafické reprezentace. Pro vybrané metody byly vytvořeny fylogenetické stromy pro porovnání přesnosti. Závěrem práce je zhodnocení získaných výsledků.

关键词： DNA sekvence numerická reprezentace grafická reprezentace CpG ostrůvky kódující sekvence podobnost dendrogram kritérium DNA sequence numerical representation graphical representation CpG islands coding sequence similarity phylogenetic tree

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The noncanonical RNA-binding protein RAN stabilizes the mRNA of intranuclear stress granule assembly factor G3BP1 in nasopharyngeal carcinoma

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JOURNAL OF BIOLOGICAL CHEMISTRY 2024年第12期300卷 107964页

作者： Yang, Pan-Yang Yang, Zhenyu Lv, Jiawei Jiang, Pei-Yi Quan, Ting-Qiu Huang, Zhuo-Hui Xu, Xu-Dong Guo, Rui Wei, Denghui Sun, Ying Sun Yat Sen Univ Guangdong Prov Clin Res Ctr Canc State Key Lab Oncol South China Guangdong Key Lab Nasopharyngeal Carcinoma Diag & Guangzhou Peoples R China Sun Yat Sen Univ Guangdong Prov Clin Res Ctr Canc Dept Radiat Oncol Canc CtrState Key Lab Oncol South ChinaGuangdong Guangzhou Peoples R China

RNA-binding proteins (RBPs) play critical roles in tumor progression by participating in the posttranscriptional regulation of RNA. However, the levels and function of RBPs in nasopharyngeal carcinoma (NPC) remain elusive. Here we identified a noncanonical RBP RAN that has the most signifi- cant role in NPC progression by a small siRNA pool screening. Functionally, RAN facilitates NPC proliferation and metastasis in vitro and in vivo. High levels of RAN are associated with poor prognosis of NPC patients and can be performed as a prognostic biomarker. Mechanistically, RAN increases the nucleus import of TDP43 and enhances TDP43 nuclear distribution. On the other hand, RAN is directly bound to the coding sequence of G3BP1 mRNA and serves as an adapter to facilitate TDP43 interacting with G3BP1 mRNA 30 UTR. These contribute to increasing G3BP1 mRNA stability in the nucleus and lead to upregulation of G3BP1, which further enhances AKT and ERK signaling and ultimately promotes NPC proliferation and metastasis. These fi ndings reveal that RAN stabilizes intranuclear G3BP1 mRNA by dual mechanisms: recruiting TDP43 into the nucleus and enhancing its interaction with G3BP1 mRNA, suggesting a critical role of RAN in NPC progression and providing a new regulation framework of RBP-RNA.

关键词： CCK-8 Cell Counting Kit-8 CDS coding sequence cDNA complementary DNA Co-IP coimmunoprecipitation GEO Gene Expression Omnibus GST glutathione- S -transferase HA hemagglutinin IF immunofluorescence IHC immunohistochemistry IP immunoprecipitation IRS immunoreactivity score MS mass spectrometry NPC nasopharyngeal carcinoma qPCR quantitative PCR RBP RNA-binding protein RIP-seq RNA immunoprecipitation sequencing RT-qPCR reverse transcription quantitative real-time PCR

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