共查询到20条相似文献,搜索用时 31 毫秒
1.
Background
The empirical frequencies of DNA k-mers in whole genome sequences provide an interesting perspective on genomic complexity, and the availability of large segments of genomic sequence from many organisms means that analysis of k-mers with non-trivial lengths is now possible. 相似文献2.
Background
Tagged sequence mutagenesis is a process for constructing libraries of sequenced insertion mutations in embryonic stem cells that can be transmitted into the mouse germline. To better predict the functional consequences of gene entrapment on cellular gene expression, the present study characterized the effects of a U3Neo gene trap retrovirus inserted into an intron of the hnRNP A2/B1 gene. The mutation was selected for analysis because it occurred in a highly expressed gene and yet did not produce obvious phenotypes following germline transmission. 相似文献3.
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Barbara Lazzari Andrea Caprera Alessandro Cestaro Ivan Merelli Marcello Del Corvo Paolo Fontana Luciano Milanesi Riccardo Velasco Alessandra Stella 《BMC plant biology》2009,9(1):82
Background
Two complete genome sequences are available for Vitis vinifera Pinot noir. Based on the sequence and gene predictions produced by the IASMA, we performed an in silico detection of putative microRNA genes and of their targets, and collected the most reliable microRNA predictions in a web database. The application is available at . 相似文献5.
Background
In this work a simple method for the computation of relative similarities between homologous metabolic network modules is presented. The method is similar to classical sequence alignment and allows for the generation of phenotypic trees amenable to be compared with correspondent sequence based trees. The procedure can be applied to both single metabolic modules and whole metabolic network data without the need of any specific assumption. 相似文献6.
Background
Over the last decade several prediction methods have been developed for determining the structural and functional properties of individual protein residues using sequence and sequence-derived information. Most of these methods are based on support vector machines as they provide accurate and generalizable prediction models. 相似文献7.
Scott Montgomerie Shan Sundararaj Warren J Gallin David S Wishart 《BMC bioinformatics》2006,7(1):301-13
Background
The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3) of about 75%. We believe this accuracy could be further improved by including structure (as opposed to sequence) database comparisons as part of the prediction process. Indeed, given the large size of the Protein Data Bank (>35,000 sequences), the probability of a newly identified sequence having a structural homologue is actually quite high. 相似文献8.
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Background
Neighboring nucleotides exert a striking influence on mutation, with the hypermutability of CpG dinucleotides in many genomes being an exemplar. Among the approaches employed to measure the relative importance of sequence neighbors on molecular evolution have been continuous-time Markov process models for substitutions that treat sequences as a series of independent tuples. The most widely used examples are the codon substitution models. We evaluated the suitability of derivatives of the nucleotide frequency weighted (hereafter NF) and tuple frequency weighted (hereafter TF) models for measuring sequence context dependent substitution. Critical properties we address are their relationships to an independent nucleotide process and the robustness of parameter estimation to changes in sequence composition. We then consider the impact on inference concerning dinucleotide substitution processes from application of these two forms to intron sequence alignments from primates. 相似文献10.
11.
Background
Whole-genome sequence alignment is an essential process for extracting valuable information about the functions, evolution, and peculiarities of genomes under investigation. As available genomic sequence data accumulate rapidly, there is great demand for tools that can compare whole-genome sequences within practical amounts of time and space. However, most existing genomic alignment tools can treat sequences that are only a few Mb long at once, and no state-of-the-art alignment program can align large sequences such as mammalian genomes directly on a conventional standalone computer. 相似文献12.
Gilles Didier Laurent Debomy Maude Pupin Ming Zhang Alexander Grossmann Claudine Devauchelle Ivan Laprevotte 《BMC bioinformatics》2007,8(1):1
Background
In general, the construction of trees is based on sequence alignments. This procedure, however, leads to loss of informationwhen parts of sequence alignments (for instance ambiguous regions) are deleted before tree building. To overcome this difficulty, one of us previously introduced a new and rapid algorithm that calculates dissimilarity matrices between sequences without preliminary alignment. 相似文献13.
Background
RNA editing is the process whereby an RNA sequence is modified from the sequence of the corresponding DNA template. In the mitochondria of land plants, some cytidines are converted to uridines before translation. Despite substantial study, the molecular biological mechanism by which C-to-U RNA editing proceeds remains relatively obscure, although several experimental studies have implicated a role for cis-recognition. A highly non-random distribution of nucleotides is observed in the immediate vicinity of edited sites (within 20 nucleotides 5' and 3'), but no precise consensus motif has been identified. 相似文献14.
Background
The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate alignments and phylogenies. Several algorithms exist based on Maximum Parsimony or Maximum Likelihood methods but many current implementations are unable to process residues with gaps, which may represent insertion/deletion (indel) events or sequence fragments. 相似文献15.
Background
Enterobacter sakazakii is an emergent pathogen that has been associated with neonatal infections through contaminated powdered infant milk formula. The species was defined by Farmer et al. (1980) who described 15 biogroups according to the biochemical characterization of 57 strains. This present study compares genotypes (DNA cluster groups based on partial 16S rDNA sequence analysis) with the biochemical traits for 189 E. sakazakii strains. 相似文献16.
Background
Conserved protein sequence regions are extremely useful for identifying and studying functionally and structurally important regions. By means of an integrated analysis of large-scale protein structure and sequence data, structural features of conserved protein sequence regions were identified. 相似文献17.
Elena Taycher Andreas Rolfs Yanhui Hu Dongmei Zuo Stephanie E Mohr Janice Williamson Joshua LaBaer 《BMC bioinformatics》2007,8(1):198
Background
Whereas the molecular assembly of protein expression clones is readily automated and routinely accomplished in high throughput, sequence verification of these clones is still largely performed manually, an arduous and time consuming process. The ultimate goal of validation is to determine if a given plasmid clone matches its reference sequence sufficiently to be "acceptable" for use in protein expression experiments. Given the accelerating increase in availability of tens of thousands of unverified clones, there is a strong demand for rapid, efficient and accurate software that automates clone validation. 相似文献18.
Antimicrobial titanium/silver PVD coatings on titanium 总被引:1,自引:0,他引:1
Andrea Ewald Susanne K Glückermann Roger Thull Uwe Gbureck 《Biomedical engineering online》2006,5(1):22-10
Background
Biofilm formation and deep infection of endoprostheses is a recurrent complication in implant surgery. Post-operative infections may be overcome by adjusting antimicrobial properties of the implant surface prior to implantation. In this work we described the development of an antimicrobial titanium/silver hard coating via the physical vapor deposition (PVD) process. 相似文献19.
Sithichoke Tangphatsornruang Prakit Somta Pichahpuk Uthaipaisanwong Juntima Chanprasert Duangjai Sangsrakru Worapa Seehalak Warunee Sommanas Somvong Tragoonrung Peerasak Srinives 《BMC plant biology》2009,9(1):137
Background
Mungbean is an important economical crop in Asia. However, genomic research has lagged behind other crop species due to the lack of polymorphic DNA markers found in this crop. The objective of this work is to develop and characterize microsatellite or simple sequence repeat (SSR) markers from genome shotgun sequencing of mungbean. 相似文献20.
Christiane Christophe-Hobertus Claude Szpirer Richard Guyon Daniel Christophe 《BMC genomics》2001,2(1):3-11