检索结果-内蒙古大学图书馆

A fractal method to distinguish coding and non-coding sequences in a complete genome based on a number sequence representation

引用

JOURNAL OF THEORETICAL BIOLOGY 2005年第4期232卷 559-567页

作者： Zhou, LQ Yu, ZG Deng, JQ Anh, V Long, SC Xiangtan Univ Sch Math & Comp Sci Xiangtan 411105 Peoples R China Queensland Univ Technol Program Stat & Operat Res Brisbane Qld 4001 Australia

A fractal method to distinguish coding and non-coding sequences in a complete genome is proposed, based on different statistical behaviors between these two kinds of sequences. We first propose a number sequence representation of DNA sequences. Multifractal analysis is then performed on the measure representation of the obtained number sequence. The three exponents C-1, C-1 and C-2 are selected from the result of multifractal analysis. Each DNA may be represented by a point in the three-dimensional space generated by these three-component vectors. It is shown that points corresponding to coding and non-coding sequences in the complete genome of many prokaryotes are roughly distributed in different regions. Fisher's discriminant algorithm can be used to separate these two regions in the spanned space. If the point (C-1,C-1,C-2) for a DNA sequence is situated in the region corresponding to coding sequences, the sequence is discriminated as a coding sequence;otherwise, the sequence is classified as a non-coding one. For all 51 prokaryotes we considered, the average discriminant accuracies p(c), p(nc), q(c), and q(nc), reach 72.28%, 84.65%, 72.53% and 84.18%, respectively. (C) 2004 Elsevier Ltd. All rights reserved.

关键词： coding sequences non-coding sequences DNA

来源：评论

学校读者我要写书评

暂无评论

Molecular evolution of duplicated ray finned fish HoxA clusters: Increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences

引用

JOURNAL OF MOLECULAR EVOLUTION 2005年第5期60卷 665-676页

作者： Wagner, GP Takahashi, K Lynch, V Prohaska, SJ Fried, C Stadler, PF Amemiya, C Yale Univ Dept Ecol & Evolutionary Biol New Haven CT 06520 USA Univ Leipzig Inst Informat D-04103 Leipzig Germany Benaroya Res Inst Virginia Mason Seattle WA USA

In this study the molecular evolution of duplicated HoxA genes in zebrafish and fugu has been investigated. All IS duplicated HoxA genes studied have a higher non-synonymous substitution rate than the corresponding genes in either bichir or paddlefish, where these genes are not duplicated. The higher rate of evolution is not due solely to a higher non-synonymous-to-synonymous rate ratio but to an increase in both the non-synonymous as well as the synonymous substitution rate. The synonymous rate increase can be explained by a change in base composition, codon usage, or mutation rate. We found no changes in nucleotide composition or codon bias. Thus, we suggest that the HoxA genes may experience an increased mutation rate following cluster duplication. In the non-Hox nuclear gene RAG] only an increase in non-synonymous substitutions could be detected, suggesting that the increased mutation rate is specific to duplicated Hox clusters and might be related to the structural instability of Hox clusters following duplication. The divergence among paralog genes tends to be asymmetric, with one paralog diverging faster than the other. In fugu, all b-paralogs diverge faster than the a-paralogs, while in zebrafish Hoxa-13a diverges faster. This asymmetry corresponds to the asymmetry in the divergence rate of conserved non-coding sequences, i.e., putative cis-regulatory elements. These results suggest that the 5 ' HoxA genes in the same cluster belong to a co-evolutionary unit in which genes have a tendency to diverge together.

关键词： duplicated HoxA genes ray finned fish synonymous substitution rate zebrafish fugu coding sequences non-coding sequences asymmetrical co-divergence

来源：评论

学校读者我要写书评

暂无评论

OrthoMaM v8: A Database of Orthologous Exons and coding sequences for Comparative Genomics in Mammals

引用

MOLECULAR BIOLOGY AND EVOLUTION 2014年第7期31卷 1923-1928页

作者： Douzery, Emmanuel J. P. Scornavacca, Celine Romiguier, Jonathan Belkhir, Khalid Galtier, Nicolas Delsuc, Frederic Ranwez, Vincent Univ Montpellier 2 UMR CNRS IRD 5554 ISE M Montpellier France Montpellier SupAgro UMR AGAP Montpellier France

Comparative genomic studies extensively rely on alignments of orthologous sequences. Yet, selecting, gathering, and aligning orthologous exons and protein-coding sequences (CDS) that are relevant for a given evolutionary analysis can be a difficult and time-consuming task. In this context, we developed OrthoMaM, a database of ORTHOlogous MAmmalian Markers describing the evolutionary dynamics of orthologous genes in mammalian genomes using a phylogenetic framework. Since its first release in 2007, OrthoMaM has regularly evolved, not only to include newly available genomes but also to incorporate up-to-date software in its analytic pipeline. This eighth release integrates the 40 complete mammalian genomes available in Ensembl v73 and provides alignments, phylogenies, evolutionary descriptor information, and functional annotations for 13,404 single-copy orthologous CDS and 6,953 long exons. The graphical interface allows to easily explore OrthoMaM to identify markers with specific characteristics (e.g., taxa availability, alignment size, %G+C, evolutionary rate, chromosome location). It hence provides an efficient solution to sample preprocessed markers adapted to user-specific needs. OrthoMaM has proven to be a valuable resource for researchers interested in mammalian phylogenomics, evolutionary genomics, and has served as a source of benchmark empirical data sets in several methodological studies. OrthoMaM is available for browsing, query and complete or filtered downloads at http://***/.

关键词： orthologous sequences mammals coding sequences phylogenomics comparative genomics

来源：评论

学校读者我要写书评

暂无评论

Complete coding sequences of dengue-1 viruses from Paraguay and Argentina

引用

VIRUS RESEARCH 2003年第1期98卷 75-82页

作者： Avilés, G Meissner, J Mantovani, R St Jeor, S Univ Nevada Dept Microbiol Reno NV 89557 USA

We have determined the complete coding sequences of six dengue-1 (DEN-1) viruses isolated from Paraguay and Argentina in 2000 from patients with dengue fever. sequences of strains 259par00, 280par00, 295arg00, 297arg00 and 301 arg00 can encode a polyprotein of 3392 amino acids. Strain 293arg00 circulated as a "wild type + deletion mutant" quasispecies, with a subpopulation characterized by a 3-nucleotide deletion in the NS4A region. This variant, which would encode a three amino acid change in the NS4A protein, was found as a minority population in one additional partially-sequenced isolate from the same outbreak. These six South American strains group into two different clades of the "American-African" DEN-1 genotype-one clade is most closely related to strains isolated from Brazil in 1997, the other to a Peruvian strain isolated in 1991 for which only partial sequence information is available. DEN-1 viruses isolated worldwide comprise at least four different genotypes according to previously defined classification criteria. (C) 2003 Elsevier B.V. All rights reserved.

关键词： dengue-1 South America coding sequences quasispecies

来源：评论

学校读者我要写书评

暂无评论

Effects of GC content and mutational pressure on the lengths of exons and coding sequences

引用

JOURNAL OF MOLECULAR EVOLUTION 2003年第3期56卷 362-370页

作者： Xia, XH Xie, Z Li, WH Univ Chicago Dept Ecol & Evolut Chicago IL 60637 USA Univ Ottawa Dept Biol Ottawa ON K1N 6N5 Canada Hunan Univ Inst Environm Protect Changsha Peoples R China

It has been hypothesized that the length of an exon tends to increase with the GC content because stop codons are AT-rich and should occur less frequently in GC-rich exons. This prediction assumes that mutation pressure plays a significant role in the occurrence and distribution of stop codons. However, the prediction is applicable not to all exons, but only to the last coding exon of a gene and to single-exon CDS sequences. We classified exons in multiexon genes in eight eukaryotic species into three groups-the first exon, the internal, and the last exon-and computed the Spearman correlation between the exon length and the percentage GC (%GC) for each of the three groups. In only five of the species studied is the correlation for the last coding exon greater than that for the first or internal exons. For the single-exon CDS sequences, the correlation between CDS length and %GC is mostly negative. Thus, eukaryotic genomes do not support the predicted relationship between exon length and %GC. In prokaryotic genomes, CDS length and %GC are positively correlated in each of the 68 completely sequenced prokaryotic genomes in GenBank with genomic GC contents varying from 25 to 68%, except for the wall-less Mycoplasma genitalium and the syphilis pathogen Treponema pallidum. Moreover, the average CDS length and the genomic GC content are also positively correlated. After correcting for genome size, the partial correlation between the average CDS length and the genomic GC content is 0.3217 (p < 0.025).

关键词： GC content exon length coding sequences mutation pressure nonsense

来源：评论

学校读者我要写书评

暂无评论

Rapid in vitro splicing of coding sequences from genomic DNA by isothermal recombination reaction-based PCR

引用

BIOTECHNOLOGY & BIOTECHNOLOGICAL EQUIPMENT 2016年第5期30卷 864-868页

作者： Chen, Wenxuan Zeng, Dongchang Shen, Rongxin Ma, Xingliang Zhang, Qunyu Chen, Letian Liu, Yao-Guang Zhu, Qinlong State Key Lab Conservat & Utilizat Subtrop Agrobi Guangzhou Guangdong Peoples R China Guangdong Prov Higher Educ Inst Key Lab Plant Funct Genom & Biotechnol Guangzhou Guangdong Peoples R China South China Agr Univ Coll Life Sci Guangzhou Guangdong Peoples R China Guangdong Prov Key Lab Prot Funct & Regulat Agr O Guangzhou Guangdong Peoples R China Univ Auckland Fac Med & Hlth Sci Auckland 1 New Zealand

Cloning of coding sequence (CDS) is an important step for gene function research. Here, we reported a simple and efficient strategy for assembling multiple-exon into an intron-free CDS from genomic DNA (gDNA) by an isothermal recombination reaction-based PCR (IRR-PCR) method. As an example, a 2067-bp full-length CDS of the anther-specific expression gene OsABCG15, which is composed of seven exons and six introns, was generated by IRR-PCR using genomic DNA of rice leaf as the template. Actually, this approach can be wildly applied to any DNA sequences assembly to achieve CDS cloning, gene fusion and multiple site-directed mutagenesis in functional genomics studies in vitro.

关键词： coding sequences DNA fragments splicing genomic DNA isothermal recombination reaction-based PCR IRR-PCR

来源：评论

学校读者我要写书评

暂无评论

THE COMPOSITIONAL DISTRIBUTION OF coding sequences AND DNA-MOLECULES IN HUMANS AND MURIDS

引用

JOURNAL OF MOLECULAR EVOLUTION 1988年第4期27卷 311-320页

作者： MOUCHIROUD, D GAUTIER, C BERNARDI, G INST JACQUES MONOD GENET MOLEC LAB 2 PL JUSSIEU F-75005 PARIS FRANCE UNIV LYON 1 BIOMETRIE LAB UNITE 243 F-69622 VILLEURBANNE FRANCE

The compositional distributions of coding sequences and DNA molecules (in the 50-100-kb range) are remarkably narrower in murids (rat and mouse) compared to humans (as well as to all other mammals explored so far). In murids, both distributions begin at higher and end at lower GC values. A comparison of homologous coding sequences from murids and humans revealed that their different compositional distributions are due to differences in GC levels in all three codon postions, particularly of genes located at both ends of the distribution. In turn, these differences are responsible for differences in both codon usage and amino acids. When GC levels at first + second codon positions and third codon positions, respectively, of murid genes are plotted against corresponding GC levels of homologous human genes, linear relationships (with very high correlation coefficients and slopes of about 0.78 and 0.60, respectively) are found. This indicates a conservation of the order of GC levels in homologous genes from humans and murids. (The same comparison for mouse and rat genes indicates a conservation of GC levels of homologous genes.) A similar linear relationship was observed when plotting GC levels of corresponding DNA fractions (as obtained by density gradient centrifugation in the presence of a sequence-specific ligand) from mouse and human. These findings indicate that orderly compositional changes affecting not only coding sequences but also noncoding sequences took place since the divergence of murids. Such directional fixations of mutations point to the existence of selective pressures affecting the genome as a whole.

关键词： Genome composition coding sequences Isochores Humans Murids

来源：评论

学校读者我要写书评

暂无评论

The length of coding sequences in a bacterial genome: Evidence for short-range correlation

引用

FLUCTUATION AND NOISE LETTERS 2007年第4期7卷 L501-L506页

作者： Zainea, Oana Morariu, Vasile V. Natl Inst Res & Dev Isotop & Mol Technol Dept Mol & Biomol Phys Cluj Napoca 400293 Romania

Series of coding sequence lengths extracted from the chromosome of Bacillus subtilis were subjected to detrended fluctuation analysis (DFA). The non-linear characteristic of the DFA plot was interpreted in terms of short-range correlation. The analysis was performed on series consisting of the whole chromosome coding sequences, as well as on the leading and lagging strands. These were compared to the same series subjected to a randomization procedure. The series were divided into two halves, which also revealed different short-range characteristics. Similar results were noticed for seven strains of Escherichia coli. Therefore, the short-range correlation characteristics are sensitive to species and strains and could be used for comparative investigations of microbial genome organization.

关键词： short-range correlation detrended fluctuation analysis coding sequences bacterial genome

来源：评论

学校读者我要写书评

暂无评论

COATi: Statistical Pairwise Alignment of Protein-coding sequences

引用

MOLECULAR BIOLOGY AND EVOLUTION 2024年第7期41卷 msae117-msae117页

作者： Mesa, Juan Jose Garcia Zhu, Ziqi Cartwright, Reed A. Arizona State Univ Biodesign Inst Tempe AZ 85281 USA Arizona State Univ Ira A Fulton Sch Engn Tempe AZ USA Arizona State Univ Sch Life Sci Tempe AZ 85281 USA

Sequence alignment is an essential method in bioinformatics and the basis of many analyses, including phylogenetic inference, ancestral sequence reconstruction, and gene annotation. Sequencing artifacts and errors made during genome assembly, such as abiological frameshifts and incorrect early stop codons, can impact downstream analyses leading to erroneous conclusions in comparative and functional genomic studies. More significantly, while indels can occur both within and between codons in natural sequences, most amino-acid- and codon-based aligners assume that indels only occur between codons. This mismatch between biology and alignment algorithms produces suboptimal alignments and errors in downstream analyses. To address these issues, we present COATi, a statistical, codon-aware pairwise aligner that supports complex insertion-deletion models and can handle artifacts present in genomic data. COATi allows users to reduce the amount of discarded data while generating more accurate sequence alignments. COATi can infer indels both within and between codons, leading to improved sequence alignments. We applied COATi to a dataset containing orthologous protein-coding sequences from humans and gorillas and conclude that 41% of indels occurred between codons, agreeing with previous work in other species. We also applied COATi to semiempirical benchmark alignments and find that it outperforms several popular alignment programs on several measures of alignment quality and accuracy.

关键词： pairwise alignment coding sequences indel phases statistical alignment codon models

来源：评论

学校读者我要写书评

暂无评论

Identifying associations between short tandem repeat sequences and gene expression in yeast reveals specific repeated motifs encoding transcriptional regulatory proteins

引用

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL 2025年 27卷 705-716页

作者： Yu, Zongyuan Liang, Yating Xiang, Meida Xu, Kang Xu, Xiang Ran, Dongyang Luo, Yawen Chen, Bijia Bo, Xiaochen Chen, Hebing Anhui Med Univ Sch Basic Med Sci Hefei 230032 Peoples R China Acad Mil Med Sci Beijing 100850 Peoples R China Shandong Univ Sch Software Shandong Peoples R China Henan Univ Sch Basic Med Sci Kaifeng Peoples R China

Tandem repeat sequences (TRs), a class of repetitive genomic elements, are broadly distributed in both coding and non-coding regions. Investigating the relationship between sequences and function is essential for understanding the genome. Saccharomyces cerevisiae serves as a vital model organism and is widely used as an engineered strain. Although the transcriptional regulatory functions of TRs in the promoters of *** have been elucidated, our understanding of their roles within coding sequences (CDS) remains limited. In this study, we integrate RNA-seq, ChIP-seq, ATAC-seq, Hi-C, and Micro-C data from *** to analyze the types and distribution of TRs, and their impact on gene expression. Our results indicate that genes containing short tandem repeats (STRs) in their CDS exhibit lower expression levels. Epigenetic analysis reveals that these regions are characterized by high levels of repressive histone modifications and low levels of activating marks, with reduced chromatin accessibility and fewer chromatin interactions. Furthermore, trinucleotide and hexanucleotide repeated motifs of STR are found primarily enriched in genes encoding transcriptional regulatory proteins. This study provides new insights into the functions and characteristics of STRs in the CDS of ***. The identification of key STR motifs offers potential targets for the design of transcriptional regulatory elements.

关键词： Short tandem repeats (STRs) Saccharomyces cerevisiae coding sequences Transcriptional regulation Epigenetic characteristic

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：