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We developed an approach for effective estimating the correlations in the noise component of gene expression data. An efficent noise reduction technique has been suggested. The resulting technique has been applied to E. coli microarray data and tested on SOS response modulated genes. 相似文献
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Correlation was observed between DNA segments characterized by periodic patterns of nucleotides and nucleosome DNA binding sites predicted by the profiles of local DNA flexibility. Exons of human type I and VII collagen genes loci have been chosen as a sample set of periodic DNA segments. It was pointed that short periodic exons coding fibrillar part of these proteins are localized near borders of the DNA sequence that binds the histone core. One of the borders of exon and of this sequence coincide as a rule. In non-fibrillar parts of collagen genes, exons (longer on average) dispose, in contrast, in any place of the DNA sequence bound to the nucleosome core. 相似文献
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V E Ramensky V J Makeev M A Roytberg V G Tumanyan 《Bioinformatics (Oxford, England)》2001,17(11):1065-1066
We present a software system BASIO that allows one to segment a sequence into regions with homogeneous nucleotide composition at a desired length scale. The system can work with arbitrary alphabet and therefore can be applied to various (e.g. protein) sequences. Several sequences of complete genomes of eukaryotes are used to demonstrate the efficiency of the software. AVAILABILITY: The BASIO suite is available for non-commercial users free of charge as a set of executables and accompanying segmentation scenarios from http://www.imb.ac.ru/compbio/basio. To obtain the source code, contact the authors. 相似文献
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Breneva NV Kiseleva EIu Makeev SM 《Zhurnal mikrobiologii, epidemiologii, i immunobiologii》2012,(3):96-102
Multi-year literature data as well as materials of the Reference centre of monitoring of natural foci infections of Irkutsk Research Institute of Plague Control of Siberia and the Far East regarding epidemiology, epizootology and laboratory diagnostics of leptospiroses in Siberia and the Far East are analyzed and summarized in the review. Situation on leptospiroses in the region has changed significantly. In 50 - 70s of the 20th century diseases were registered ubiquitously in the form of outbreaks, group and single cases. Currently a low level of sporadic morbidity is noted in separate subjects of the Russian Federation. The contemporary state of the problem remains insufficiently clear, this demands the expansion of studies, creation of modern databases, as well as introduction into the practice of highly sensitive methods of express diagnostics in a complex with bacteriologic and serologic methods. 相似文献
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Favorov A Mularoni L Cope LM Medvedeva Y Mironov AA Makeev VJ Wheelan SJ 《PLoS computational biology》2012,8(5):e1002529
We have created a statistically grounded tool for determining the correlation of genomewide data with other datasets or known biological features, intended to guide biological exploration of high-dimensional datasets, rather than providing immediate answers. The software enables several biologically motivated approaches to these data and here we describe the rationale and implementation for each approach. Our models and statistics are implemented in an R package that efficiently calculates the spatial correlation between two sets of genomic intervals (data and/or annotated features), for use as a metric of functional interaction. The software handles any type of pointwise or interval data and instead of running analyses with predefined metrics, it computes the significance and direction of several types of spatial association; this is intended to suggest potentially relevant relationships between the datasets. AVAILABILITY AND IMPLEMENTATION: The package, GenometriCorr, can be freely downloaded at http://genometricorr.sourceforge.net/. Installation guidelines and examples are available from the sourceforge repository. The package is pending submission to Bioconductor. 相似文献
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Regions with a quasiperiodical location of exon--intron sites have been found in the loci of genes of I and VII type collagens (with a total length of exons more than 15% of the entire size of the locus). The periods observed are similar to periods typical for the nucleosomal level of the organization of chromatin. It was shown that the sites consisting of successively arranged exons and introns form groups involving two to five such regions of the same length. The groups encoding the fibrillar regions of the gene product contain more than 50% of exons. The regions are on the average 165 nt long, which is close to the minimal nucleosomal repeat length observed in some regions of the eukaryotic genome. In the nonfibrillar region of the gene of VII type collagen, groups of several exon-intron pairs with an average length of 227 nt were identified. The change in the length of exon-introns sites on going from the nonfibrillar to the fibrillar moiety occurs in a jump, which is clearly seen on a periodogram of the locus. 相似文献
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Transmembrane transport is an essential component of the cell life. Many genes encoding known or putative transport proteins are found in bacterial genomes. In most cases their substrate specificity is not experimentally determined and only approximately predicted by comparative genomic analysis. Even less is known about the 3D structure of transporters. Nevertheless, the published experimental data demonstrate that channel-forming residues determine the substrate specificity of secondary transporters and analysis of these residues would provide better understanding of the transport mechanism. We developed a simple computational method for identification of channel-forming residues in transporter sequences. It is based on the analysis of amino acids frequencies in bacterial secondary transporters. We applied this method to a variety of transmembrane proteins with resolved 3D structure. The predictions are in sufficiently good agreement with the real protein structure. 相似文献