检索结果-内蒙古大学图书馆

Statistics of trinucleotides in coding sequences and evolution

JOURNAL OF THEORETICAL BIOLOGY 2003年第2期222卷 139-149页

作者： Takeuchi, F Futamura, Y Yoshikura, H Yamamoto, K Int Med Ctr Japan Res Inst Shinjuku Ku Tokyo 1628655 Japan Org Pharmaceut Safety & Res Tokyo 1000013 Japan

The aim of this paper is to give measurements indicative of evolutional stages of the species. Two types of statistics of trinucleotides in coding regions are analysed for 27 species. The first one is the codon space, the nucleotide ratio for each of the three codon positions. We apply principal component analysis on this space and extract two principal components faithfully describing the original distribution of the codon space. The first principal component corresponds to. the GC content. The second principal component classifies the species into three evolutional groups, Archaea, Bacteria and Eukaryota. The second statistics is the real and theoretical frequency of amino acids, The real frequency of an amino acid in a coding sequence is its frequency in the translated protein. The theoretical frequency is the expected frequency calculated from the ratio of nucleotides. We introduce the discrepancy between these two frequencies as an index of non-randomness of nucleotides in the sequence. This index of non-randomness divides the species into two groups: eukaryotes having smaller non-randomness (i.e. being more random) and prokaryotes having higher non-randomness. (C) 2003 Elsevier Science Ltd. All rights reserved.

关键词： statistics of trinucleotides coding sequence codon space principal component analysis theoretical amino acid frequency randomness codon usage tRNA abundance evolution

来源：评论

学校读者我要写书评

暂无评论

Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics

引用

JOURNAL OF PROTEOMICS 2013年 86卷 27-42页

作者： Mueller, Stephan A. Findeiss, Sven Pernitzsch, Sandy R. Wissenbach, Dirk K. Stadler, Peter F. Hofacker, Ivo L. von Bergen, Martin Kalkhof, Stefan UFZ Helmholtz Ctr Environm Res Leipzig Dept Prote D-04318 Leipzig Germany Univ Vienna Inst Theoret Chem A-1090 Vienna Austria Univ Vienna Bioinformat & Computat Biol Res Grp A-1090 Vienna Austria Univ Wurzburg Res Ctr Infect Dis ZINF D-97070 Wurzburg Germany UFZ Helmholtz Ctr Environm Res Leipzig Dept Metabol D-04318 Leipzig Germany Univ Leipzig Dept Comp Sci Bioinformat Grp D-04107 Leipzig Germany Fraunhofer Inst Cell Therapy & Immunol RNom Grp D-04103 Leipzig Germany Santa Fe Inst Santa Fe NM 87501 USA Max Planck Inst Math Sci D-04103 Leipzig Germany Aalborg Univ Dept Biotechnol Chem & Environm Engn DK-9000 Aalborg Denmark

Correct annotation of protein coding genes is the basis of conventional data analysis in proteomic studies. Nevertheless, most protein sequence databases almost exclusively rely on gene finding software and inevitably also miss protein annotations or possess errors. Proteogenomics tries to overcome these issues by matching MS data directly against a genome sequence database. Here we report an in-depth proteogenomics study of Helicobacter pylon strain 26695. MS data was searched against a combined database of the NCBI annotations and a six-frame translation of the genome. Database searches with Mascot and X! Tandem revealed 1115 proteins identified by at least two peptides with a peptide false discovery rate below 1%. This represents 71% of the predicted proteome. So far this is the most extensive proteome study of Helicobacter pylon. Our proteogenomic approach unambiguously identified four previously missed annotations and furthermore allowed us to correct sequences of six annotated proteins. Since secreted proteins are often involved in pathogenic processes we further investigated signal peptidase cleavage sites. By applying a database search that accommodates the identification of semi-specific cleaved peptides, 63 previously unknown signal peptides were detected. The motif LXA showed to be the predominant recognition sequence for signal peptidases. Biological significance The results of MS-based proteomic studies highly rely on correct annotation of protein coding genes which is the basis of conventional data analysis. However, the annotation of protein coding sequences in genomic data is usually based on gene finding software. These tools are limited in their prediction accuracy such as the problematic determination of exact gene boundaries. Thus, protein databases own partly erroneous or incomplete sequences. Additionally, some protein sequences might also be missing in the databases. Proteogenomics, a combination of proteomic and genomic data analyses, is well

关键词： Proteogenomics Proteomics coding sequence Helicobacter pylori Signal peptide

来源：评论

学校读者我要写书评

暂无评论

Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector

引用

NUCLEIC ACIDS RESEARCH 2007年第7期35卷 E47-1-E47-6-0页

作者： Fredriksson, Simon Baner, Johan Dahl, Fredrik Chu, Angela Ji, Hanlee Welch, Katrina Davis, Ronald W. Stanford Genome Technol Ctr Bio X Stanford CA 94305 USA

Herein we present Gene-Collector, a method for multiplex amplification of nucleic acids. The procedure has been employed to successfully amplify the coding sequence of 10 human cancer genes in one assay with uniform abundance of the final products. Amplification is initiated by a multiplex PCR in this case with 170 primer pairs. Each PCR product is then specifically circularized by ligation on a Collector probe capable of juxtapositioning only the perfectly matched cognate primer pairs. Any amplification artifacts typically associated with multiplex PCR derived from the use of many primer pairs such as false amplicons, primer-dimers etc. are not circularized and degraded by exonuclease treatment. Circular DNA molecules are then further enriched by randomly primed rolling circle replication. Amplification was successful for 90% of the targeted amplicons as seen by hybridization to a custom resequencing DNA micro-array. Real-time quantitative PCR revealed that 96% of the amplification products were all within 4-fold of the average abundance. Gene-Collector has utility for numerous applications such as high throughput resequencing, SNP analyses, and pathogen detection.

关键词： MISMATCH REPAIR DETECTION DNA FRAGMENTS PCR Multiplex Polymerase Chain Reaction DNA fragment coding sequence Oncogenes

来源：评论

学校读者我要写书评

暂无评论

Molecular characterization of coding sequences and analysis of toll-like receptor 3 mRNA expression in water buffalo (Bubalus bubalis) and nilgai (Boselaphus tragocamelus)

引用

IMMUNOGENETICS 2007年第1期59卷 69-76页

作者： Dhara, Animesh Saini, Mohini Das, Dhanjit K. Swarup, Devendra Sharma, Bhaskar Kumar, Satish Gupta, Praveen K. Indian Vet Res Inst Ctr Wildlife Izatnagar 243122 Uttar Pradesh India Indian Vet Res Inst Div Biochem Izatnagar 243122 Uttar Pradesh India Indian Vet Res Inst Div Vet Biotechnol Izatnagar 243122 Uttar Pradesh India

Toll-like receptor 3 (TLR3), an antiviral innate immunity receptor recognizes double-stranded RNA, preferably of viral origin and induces type I interferon production, which causes maturation of phagocytes and subsequent release of chemical mediators from phagocytes against some viral infections. The present study has characterized TLR3 complementary DNA (cDNA) in buffalo (Bubalus bubalis) and nilgai (Boselaphus tragocamelus). TLR3 coding sequences of both buffalo and nilgai were amplified from cultured dendritic cell cDNA and cloned in pGEMT-easy vector for characterization by restriction endonucleases and nucleotide sequencing. sequence analysis reveals that 2,715-bp-long TLR3 open reading frame encoding 904 amino acids in buffalo as well as nilgai is similar to that of cattle. Buffalo TLR3 has 98.6 and 97.9% identity at nucleotide level with nilgai and cattle, respectively. Likewise, buffalo TLR3 amino acids share 96.7% identity with cattle and 97.8% with nilgai. Non-synonymous substitutions exceeding synonymous substitutions indicate evolution of this receptor through positive selection among these three ruminant species. Buffalo and nilgai appear to have diverged from a common ancestor in phylogenetic analysis. Predicted protein structures of buffalo and nilgai TLR3 from deduced amino acid sequences indicate that the buffalo and nilgai TLR3 ectodomain may be more efficient in ligand binding than that of cattle. Furthermore, TLR3 messenger RNA expression in tissues as quantified by real-time PCR was found higher in nilgai than buffalo.

关键词： toll-like receptor 3 innate immunity Bubalus bubalis Boselaphus tragocamelus coding sequence

来源：评论

学校读者我要写书评

暂无评论

Differential mRNA fingerprinting by preferential amplification of coding sequences

引用

GENE 2000年第1-2期258卷 155-163页

作者： Fuchs, B Zhang, KB Bolander, ME Sarkar, G Mayo Clin Rochester MN 55905 USA

The need for rapid identification of differentially expressed genes will persist even after the complete human genomic sequence becomes available. The most popular method for identifying differentially expressed genes acquires expressed sequence tags (ESTs) from the extreme 3' non-coding end of mRNAs. Such ESTs have limitations for downstream applications. We have developed a method, termed preferential amplification of coding sequences (PACS), that was applied to identify differentially expressed coding sequence tags (dCSTs) between osteoblasts and osteosarcoma cells. PACS was achieved by PCR with a set of primers to anchor at sequences complementary to AUG sequences in mRNAs and another set of primers to anchor at a PCR-amplifiable distance from AUG sequences. An initial screen identified 103 candidate dCSTs after screening similar to 15% of the expressed genes between the two cell types. Of these sequences, 27 represent CSTs of known genes and two are from 3'-ESTs of known mRNAs. Thus, PACS identified CSTs similar to 13.5 times more often than it identified 3' ESTs, attesting to the objective of the method. Since many of the dCSTs represent known genes, their identity and potential relevance to osteosarcoma could be immediately hypothesized. Differential expression of many of the dCSTs was further demonstrated by northern blotting or RT-PCR. Since PACS is not dependent on the existence of a poly A tail on an mRNA, it should have application to identify dCSTs for both prokaryotic and eukaryotic organisms. Additionally, PACS should aid in the identification of cell-specific or tissue-specific genes and bidirectional acquisition of cDNA sequence enabling rapid retrieval of full-length cDNA sequence of novel genes. (C) 2000 Elsevier Science B.V. All rights reserved.

关键词： coding sequence differential gene expression double restriction site primers osteosarcoma preferential amplification sequence tags

来源：评论

学校读者我要写书评

暂无评论

TransTerm, the translational signal database, extended to include full coding sequences and untranslated regions

引用

NUCLEIC ACIDS RESEARCH 1999年第1期27卷 293-294页

作者： Dalphin, ME Stockwell, PA Tate, WP Brown, CM Univ Otago Dept Biochem Dunedin New Zealand

TransTerm is a database of mRNA sequences and parameters useful for detecting translational control signals in general. TransTerm-98 has been expanded beyond previous years to include full coding sequences and UTRs, while retaining the original small contexts about the coding sequence start- and stop-codons. The database contains more than 130 000 non-redundant coding sequences with associated untranslated regions (UTRs) from over 450 species. This includes the complete genomes of 12 prokaryotic and one eukaryotic organism. Several coding sequence parameters are available: coding sequence length, Nc, GC3 and, when it is computable. Codon Adaptation index (CAI). Codon usage tables and summaries of start- and stop-codon contexts are also included. TransTerm-98 has both a relational database form with a WWW interface and a flatfile format, also available by Internet browser. TransTerm is available at: http://***:800/Transterm/***.

关键词： .format codon UTRs includes coding sequence relational translational signal database TransTerm full coding

来源：评论

学校读者我要写书评

暂无评论

Detection of Mammalian coding sequences Using a Hybrid Approach of Chaos Game Representation and Machine Learning

Detection of Mammalian Coding Sequences Using a Hybrid Appro...

引用

IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM)

作者： Emam, Mohamed Ali, Amna Abdelrazik, Eman Elattar, Mustafa El-Hadidi, Mohamed Nile Univ Ctr Informat Sci Giza Egypt Nile Univ Sch Informat Technol & Comp Sci ITCS Giza Egypt

ISBN: (纸本)9781728162157

Mammalian protein-coding sequence detection provides a wide range of applications in biodiversity research, evolutionary studies, and understanding of genomic features. Representation of genomic sequences in Chaos Game Representation (CGR) helps reveal hidden features in DNA sequences due to its ability to represent sequences in both numerical and graphical levels. Machine learning approaches can automatically detect hidden patterns in CGR images by detecting and classifying protein-coding and non-coding patterns accurately. Here, we propose a pipeline that automatically detects coding (exons) and non-coding (intron) sequences in mammalian genomes. We collected coding and non-coding sequences from 20 mammalian-specific genes (PRM3, CSN1S1, LCE6A, IL2, MUC7, NNAT, IGIP, SMCP, DCD, and MYEOV), and GCR images were generated from these genes. Five supervised machine learning classifier algorithms (Naive Bayes algorithm, Logistic Regression algorithm, K-Nearest Neighbor algorithm, Perceptron algorithm, and support vector machine (SVM)) were evaluated, using features extracted from CGR images as an input. In Summary, the Ensemble model between Logistic regression, perceptron and SVM has achieved the highest accuracy with a mean performance of mean and standard deviation. Our findings recommend applying an ensemble model between Logistic regression, Perceptron and SVM for classifying coding and non-coding sequences for future mammalian related CGR genomic studies.

关键词： coding sequence intron supervised machine learning Support Vector Machine chaos game representation

来源：评论

学校读者我要写书评

暂无评论

A Database of Potential Reading Frame Shifts in coding sequences from Different Eukaryotic Genomes

引用

Biophysics (Russian Federation) 2019年第3期64卷 339-348页

作者： Suvorova, Yu. M. Pugacheva, V.M. Korotkov, E.V. Research Center of Biotechnology Russian Academy of Sciences Moscow 119071 Russian Federation Moscow Engineering Physics Institute National Research Nuclear University (MEPhI) Moscow 115409 Russian Federation

Abstract—A new data bank containing potential reading frame shifts was developed. A new mathematical method based on the use of the genetic algorithm and dynamic programming was used to search for potential reading frame shifts. The data bank includes coordinates of potential reading frame shifts for coding sequences of 76 eukaryotic genomes from the Ensembl genome browser version 86. The database is located at: http://***/cgi-bin/frameshift/***. Among all the analyzed genomes approximately 23% of the coding sequences have a reading frame shift. Type I and type II errors are at levels of approximately 11 and 30%. A Web server to search for potential reading frame shifts, which is located at: http://***/fsfinder, was developed simultaneously with the data bank. The server can be used to search for potential reading frame shifts in newly defined coding sequences. © 2019, Pleiades Publishing, Inc.

关键词： coding sequence dynamic programming Keywords: reading frame shift position weight matrix

来源：评论

学校读者我要写书评

暂无评论

The Application of Nicotiana benthamiana as a Transient Expression Host to Clone the coding sequences of Plant Genes

引用

American Journal of Molecular Biology 2024年第2期14卷 54-65页

作者： Jianzhong Huang Peng Jia Xiaoju Zhong Xiuying Guan Hongbin Zhang Honglei Ruan Key Laboratory of Chronic Diseases Fuzhou Medical University Fuzhou China

coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using complementary DNA (cDNA) derived from messenger RNA (mRNA) extracted from plant tissues and generated by reverse transcription. However, some CDS are difficult to acquire through this process as they are expressed at extremely low levels or have specific spatial and/or temporal expression patterns in vivo. These challenges require the development of alternative CDS cloning technologies. In this study, we found that the genomic intron-containing gene coding sequences (gDNA) from Arabidopsis thaliana, Oryza sativa, Brassica napus, and Glycine max can be correctly transcribed and spliced into mRNA in Nicotiana benthamiana. In contrast, gDNAs from Triticum aestivum and Sorghum bicolor did not function correctly. In transient expression experiments, the target DNA sequence is driven by a constitutive promoter. Theoretically, a sufficient amount of mRNA can be extracted from the N. benthamiana leaves, making it conducive to the cloning of CDS target genes. Our data demonstrate that N. benthamiana can be used as an effective host for the cloning CDS of plant genes.

关键词： coding sequence Genomic sequence Nicotiana benthamiana Plant Genes

来源：评论

学校读者我要写书评

暂无评论

A resource of human coronavirus protein-coding sequences in a flexible, multipurpose Gateway Entry clone collection

引用

G3-GENES GENOMES GENETICS 2023年第7期13卷 jkad105页

作者： Weller, Benjamin Lin, Chung-Wen Pogoutse, Oxana Sauer, Mayra de la Rosa, Nora Strobel, Alexandra Young, Veronika Knapp, Jennifer J. Rayhan, Ashyad Falter, Claudia Kim, Dae-Kyum Roth, Frederick P. Falter-Braun, Pascal Helmholtz Zentrum Munchen Inst Network Biol INET Mol Targets & Therapeut Ctr MTTC German Res Ctr Environm Hlth Ingolstadter Landstr 1 D-85764 Neuherberg Germany Univ Toronto Donnelly Ctr Cellular & Biomol Res CCBR 160 Coll St Toronto ON M5S 3E1 Canada Univ Toronto Dept Mol Genet 1 Kings Coll Cir Toronto ON M5S 1A8 Canada Sinai Hlth Syst Lunenfeld Tanenbaum Res Inst LTRI 600 Univ Ave Toronto ON M5G 1X5 Canada Dana Farber Canc Inst Ctr Canc Syst Biol CCSB 450 Brookline Ave Boston MA 02215 USA Roswell Park Comprehens Canc Ctr Dept Canc Genet & Genom Elm & Carlton St Buffalo NY 14263 USA Univ Toronto Dept Comp Sci 40 St George St Toronto ON M5S 2E4 Canada Ludwig Maximilians Univ LMU Munchen Fac Biol Microbe Host Interact Grosshaderner Str 9 D-82152 Martinsried Germany Helmholtz Zentrum Munchen Inst Network Biol Ingolstadter Landstr 1 D-85764 Neuherberg Germany Univ Toronto Donnelly Ctr 160 Coll St Toronto ON M5S 3E1 Canada

The COVID-19 pandemic has catalyzed unprecedented scientific data and reagent sharing and collaboration, which enabled understanding the virology of the SARS-CoV-2 virus and vaccine development at record speed. The pandemic, however, has also raised awareness of the danger posed by the family of coronaviruses, of which 7 are known to infect humans and dozens have been identified in reservoir species, such as bats, rodents, or livestock. To facilitate understanding the commonalities and specifics of coronavirus infections and aspects of viral biology that determine their level of lethality to the human host, we have generated a collection of freely available clones encoding nearly all human coronavirus proteins known to date. We hope that this flexible, Gateway-compatible vector collection will encourage further research into the interactions of coronaviruses with their human host, to increase preparedness for future zoonotic viral outbreaks.

关键词： coronavirus HCoV coding sequence SARS-CoV-2 OC43 MERS HKU1 229E NL63 Gateway Entry clone

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：