共查询到20条相似文献,搜索用时 31 毫秒
1.
Marian Thieme Claudio Lottaz Harald Niederst?tter Walther Parson Rainer Spang Peter J Oefner 《BMC bioinformatics》2009,10(1):440
Background
The Affymetrix MitoChip v2.0 is an oligonucleotide tiling array for the resequencing of the human mitochondrial (mt) genome. For each of 16,569 nucleotide positions of the mt genome it holds two sets of four 25-mer probes each that match the heavy and the light strand of a reference mt genome and vary only at their central position to interrogate all four possible alleles. In addition, the MitoChip v2.0 carries alternative local context probes to account for known mtDNA variants. These probes have been neglected in most studies due to the lack of software for their automated analysis. 相似文献2.
Background
When there are no strand-specific biases in mutation and selection rates (that is, in the substitution rates) between the two strands of DNA, the average nucleotide composition is theoretically expected to be A = T and G = C within each strand. Deviations from these equalities are therefore evidence for an asymmetry in selection and/or mutation between the two strands. By focusing on weakly selected regions that could be oriented with respect to replication in 43 out of 51 completely sequenced bacterial chromosomes, we have been able to detect asymmetric directional mutation pressures.Results
Most of the 43 chromosomes were found to be relatively enriched in G over C and T over A, and slightly depleted in G+C, in their weakly selected positions (intergenic regions and third codon positions) in the leading strand compared with the lagging strand. Deviations from A = T and G = C were highly correlated between third codon positions and intergenic regions, with a lower degree of deviation in intergenic regions, and were not correlated with overall genomic G+C content.Conclusions
During the course of bacterial chromosome evolution, the effects of asymmetric directional mutation pressures are commonly observed in weakly selected positions. The degree of deviation from equality is highly variable among species, and within species is higher in third codon positions than in intergenic regions. The orientation of these effects is almost universal and is compatible in most cases with the hypothesis of an excess of cytosine deamination in the single-stranded state during DNA replication. However, the variation in G+C content between species is influenced by factors other than asymmetric mutation pressure.3.
Claudine Montgelard Ellen Forty Véronique Arnal Conrad A Matthee 《BMC evolutionary biology》2008,8(1):321
Background
The number of rodent clades identified above the family level is contentious, and to date, no consensus has been reached on the basal evolutionary relationships among all rodent families. Rodent suprafamilial phylogenetic relationships are investigated in the present study using ~7600 nucleotide characters derived from two mitochondrial genes (Cytochrome b and 12S rRNA), two nuclear exons (IRBP and vWF) and four nuclear introns (MGF, PRKC, SPTBN, THY). Because increasing the number of nucleotides does not necessarily increase phylogenetic signal (especially if the data is saturated), we assess the potential impact of saturation for each dataset by removing the fastest-evolving positions that have been recognized as sources of inconsistencies in phylogenetics. 相似文献4.
Jason C Ting Ying Ye George H Thomas Ingo Ruczinski Jonathan Pevsner 《BMC bioinformatics》2006,7(1):25-21
Background
A variety of diseases are caused by chromosomal abnormalities such as aneuploidies (having an abnormal number of chromosomes), microdeletions, microduplications, and uniparental disomy. High density single nucleotide polymorphism (SNP) microarrays provide information on chromosomal copy number changes, as well as genotype (heterozygosity and homozygosity). SNP array studies generate multiple types of data for each SNP site, some with more than 100,000 SNPs represented on each array. The identification of different classes of anomalies within SNP data has been challenging. 相似文献5.
Background
Multiple approaches for the site-directed mutagenesis (SDM) have been developed. However, only several of them are designed for simultaneous introduction of multiple nucleotide alterations, and these are time consuming. In addition, many of the existing multiple SDM methods have technical limitations associated with type and number of mutations that can be introduced, or are technically demanding and require special chemical reagents. 相似文献6.
Weiwu Jin Jason R Grant Paul Stothard Stephen S Moore Le Luo Guan 《BMC molecular biology》2009,10(1):90
Background
MicroRNAs (miRNAs) are a family of ~22 nucleotide small RNA molecules which regulate gene expression by fully or partially binding to their complementary sequences in mRNAs or promoters. A large number of miRNAs and their expression patterns have been reported in human, mouse and rat. However, miRNAs and their expression patterns in live stock species such as beef cattle are not well studied. 相似文献7.
Background
We have compared 38 isolates of the SARS-CoV complete genome. The main goal was twofold: first, to analyze and compare nucleotide sequences and to identify positions of single nucleotide polymorphism (SNP), insertions and deletions, and second, to group them according to sequence similarity, eventually pointing to phylogeny of SARS-CoV isolates. The comparison is based on genome polymorphism such as insertions or deletions and the number and positions of SNPs. 相似文献8.
Predicting protein-protein interactions in unbalanced data using the primary structure of proteins 总被引:1,自引:0,他引:1
Background
Elucidating protein-protein interactions (PPIs) is essential to constructing protein interaction networks and facilitating our understanding of the general principles of biological systems. Previous studies have revealed that interacting protein pairs can be predicted by their primary structure. Most of these approaches have achieved satisfactory performance on datasets comprising equal number of interacting and non-interacting protein pairs. However, this ratio is highly unbalanced in nature, and these techniques have not been comprehensively evaluated with respect to the effect of the large number of non-interacting pairs in realistic datasets. Moreover, since highly unbalanced distributions usually lead to large datasets, more efficient predictors are desired when handling such challenging tasks. 相似文献9.
Louis-Philippe Lemieux Perreault Gregor U Andelfinger Géraldine Asselin Marie-Pierre Dubé 《BMC bioinformatics》2010,11(1):226
Background
Copy number variations (CNVs) and polymorphisms (CNPs) have only recently gained the genetic community's attention. Conservative estimates have shown that CNVs and CNPs might affect more than 10% of the genome and that they may be at least as important as single nucleotide polymorphisms in assessing human variability. Widely used tools for CNP analysis have been implemented in Birdsuite and PLINK for the purpose of conducting genetic association studies based on the unpartitioned total number of CNP copies provided by the intensities from Affymetrix's Genome-Wide Human SNP Array. Here, we are interested in partitioning copy number variations and polymorphisms in extended pedigrees for the purpose of linkage analysis on familial data. 相似文献10.
Background
The CyaB protein from Aeromonas hydrophila has been shown to possess adenylyl cyclase activity. While orthologs of this enzyme have been found in some bacteria and archaea, it shows no detectable relationship to the classical nucleotide cyclases. Furthermore, the actual biological functions of these proteins are not clearly understood because they are also present in organisms in which there is no evidence for cyclic nucleotide signaling. 相似文献11.
P Andrew Nevarez Christopher M DeBoever Benjamin J Freeland Marissa A Quitt Eliot C Bush 《BMC bioinformatics》2010,11(1):462
Background
Models of sequence evolution typically assume that different nucleotide positions evolve independently. This assumption is widely appreciated to be an over-simplification. The best known violations involve biases due to adjacent nucleotides. There have also been suggestions that biases exist at larger scales, however this possibility has not been systematically explored. 相似文献12.
Patrick M O'Grady Richard H Baker Celeste M Durando William J Etges Robert DeSalle 《BMC evolutionary biology》2001,1(1):6-6
Background
Polytene chromosome banding patterns have long been used by Drosophila evolutionists to infer degree of relatedness among taxa. Recently, nucleotide sequences have preempted this traditional method. We place the classical Drosophila evolutionary biology tools of polytene chromosome inversion analysis in a phylogenetic context and assess their utility in comparison to nucleotide sequences. 相似文献13.
Background
As the number of non-synonymous single nucleotide polymorphisms (nsSNPs), also known as single amino acid polymorphisms (SAPs), increases rapidly, computational methods that can distinguish disease-causing SAPs from neutral SAPs are needed. Many methods have been developed to distinguish disease-causing SAPs based on both structural and sequence features of the mutation point. One limitation of these methods is that they are not applicable to the cases where protein structures are not available. In this study, we explore the feasibility of classifying SAPs into disease-causing and neutral mutations using only information derived from protein sequence. 相似文献14.
Mackie C. O'Hara W. Scott McGraw Debbie Guatelli-Steinberg 《American journal of physical anthropology》2023,180(3):519-533
Objectives
Developmental defects of tooth enamel are associated with systemic physiological stress and have been linked to seasonal environmental factors such as rainfall, temperature, and fruit availability. Here, we evaluate whether linear enamel hypoplasia and accentuated perikymata occur with any cyclicity on lower canines and then whether cycles differ between Bornean and Sumatran orangutans.Materials and Methods
Epoxy casts of lower canines from Pongo abelii (n = 14) and P. pygmaeus (n = 33) were evaluated for perikymata and dental enamel defects. Individual developmental sequences (IDSs) were generated for each canine, tracking the position of each defect in the context of continuous perikymata (time). Autocorrelation, a form of time-series statistical analysis was run for each canine to identify whether any cyclicity of defect expression was discernable.Results
Autocorrelation revealed cycles of defect expression within canines, but no common cycle periodicities were identified between individuals of the same species or across species. P. pygmaeus averaged more linear enamel hypoplasia per year than P. abelli, but no other comparisons (number of defects, number of perikymata between defects, and autocorrelation analysis) revealed differences between the species.Discussion
Although no common patterns of defect expression were identified within or between P. abelli and P. pygmaeus, the potential for autocorrelation analysis is promising for primatological and paleoanthropological studies of seasonal phenomena.15.
Alejandro Cáceres Suzanne S Sindi Benjamin J Raphael Mario Cáceres Juan R González 《BMC bioinformatics》2012,13(1):28
Background
Polymorphic inversions are a source of genetic variability with a direct impact on recombination frequencies. Given the difficulty of their experimental study, computational methods have been developed to infer their existence in a large number of individuals using genome-wide data of nucleotide variation. Methods based on haplotype tagging of known inversions attempt to classify individuals as having a normal or inverted allele. Other methods that measure differences between linkage disequilibrium attempt to identify regions with inversions but unable to classify subjects accurately, an essential requirement for association studies. 相似文献16.
Background
Millions of single nucleotide polymorphisms have been identified as a result of the human genome project and the rapid advance of high throughput genotyping technology. Genetic association studies, such as recent genome-wide association studies (GWAS), have provided a springboard for exploring the contribution of inherited genetic variation and gene/environment interactions in relation to disease. Given the capacity of such studies to produce a plethora of information that may then be described in a number of publications, selecting possible disease susceptibility genes and identifying related modifiable risk factors is a major challenge. A Web-based application for finding evidence of such relationships is key to the development of follow-up studies and evidence for translational research. 相似文献17.
Background
Genome-wide association study (GWAS) aims to find genetic factors underlying complex phenotypic traits, for which epistasis or gene-gene interaction detection is often preferred over single-locus approach. However, the computational burden has been a major hurdle to apply epistasis test in the genome-wide scale due to a large number of single nucleotide polymorphism (SNP) pairs to be tested. 相似文献18.
19.
Judita Mascarenhas Humberto Sanchez Serkalem Tadesse Dawit Kidane Mahalakshmi Krisnamurthy Juan C Alonso Peter L Graumann 《BMC molecular biology》2006,7(1):20-15
Background
Several distinct pathways for the repair of damaged DNA exist in all cells. DNA modifications are repaired by base excision or nucleotide excision repair, while DNA double strand breaks (DSBs) can be repaired through direct joining of broken ends (non homologous end joining, NHEJ) or through recombination with the non broken sister chromosome (homologous recombination, HR). Rad50 protein plays an important role in repair of DNA damage in eukaryotic cells, and forms a complex with the Mre11 nuclease. The prokaryotic ortholog of Rad50, SbcC, also forms a complex with a nuclease, SbcD, in Escherichia coli, and has been implicated in the removal of hairpin structures that can arise during DNA replication. Ku protein is a component of the NHEJ pathway in pro- and eukaryotic cells. 相似文献20.
Carlo Alviggi Peter Humaidan Colin M Howles Donald Tredway Stephen G Hillier 《Reproductive biology and endocrinology : RB&E》2009,7(1):101-13