共查询到20条相似文献,搜索用时 15 毫秒
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Background
We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect of the length distribution of fragments. We also introduce a coding of the shape of the coverage depth function as a tree and explain how this can be used to detect regions with anomalous coverage. This modeling perspective is especially germane to current high-throughput sequencing experiments, where both sample preparation protocols and sequencing technology particulars can affect fragment length distributions. 相似文献3.
Lee A Newberg 《BMC bioinformatics》2009,10(1):212
Background
Hidden Markov models and hidden Boltzmann models are employed in computational biology and a variety of other scientific fields for a variety of analyses of sequential data. Whether the associated algorithms are used to compute an actual probability or, more generally, an odds ratio or some other score, a frequent requirement is that the error statistics of a given score be known. What is the chance that random data would achieve that score or better? What is the chance that a real signal would achieve a given score threshold? 相似文献4.
Omar JM Hamza Mecky IN Matee Mainen J Moshi Elison NM Simon Ferdinand Mugusi Frans HM Mikx Wim H van Palenstein Helderman Antonius JMM Rijs André JAM van der Ven Paul E Verweij 《BMC microbiology》2008,8(1):135
Background
In Tanzania, little is known on the species distribution and antifungal susceptibility profiles of yeast isolates from HIV-infected patients with primary and recurrent oropharyngeal candidiasis. 相似文献5.
Background
The choice of probe set algorithms for expression summary in a GeneChip study has a great impact on subsequent gene expression data analysis. Spiked-in cRNAs with known concentration are often used to assess the relative performance of probe set algorithms. Given the fact that the spiked-in cRNAs do not represent endogenously expressed genes in experiments, it becomes increasingly important to have methods to study whether a particular probe set algorithm is more appropriate for a specific dataset, without using such external reference data. 相似文献6.
Background
Metagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the potential to identify significantly different metabolic potential in different environments. 相似文献7.
Background
One way in which positional information is established during embryonic development is through the graded distribution of diffusible morphogens. Unfortunately, little is known about how cells interpret different concentrations of morphogen to activate different genes or how thresholds are generated in a morphogen gradient. 相似文献8.
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Alessio Valletta Livio Trainotti Anna Rita Santamaria Gabriella Pasqua 《BMC plant biology》2010,10(1):69
Background
Camptotheca acuminata is a major natural source of the terpenoid indole alkaloid camptothecin (CPT). At present, little is known about the cellular distribution of the biosynthesis of CPT, which would be useful knowledge for developing new strategies and technologies for improving alkaloid production. 相似文献10.
Marcelo Filonzi Laís C Cardoso Maristela T Pimenta Daniel BC Queiróz Maria CW Avellar Catarina S Porto Maria FM Lazari 《Reproductive biology and endocrinology : RB&E》2007,5(1):29
Background
Relaxin is the endogenous ligand of the G-protein coupled receptor RXFP1, previously known as LGR7. In humans relaxin can also activate, but with lower affinity, the closely related receptor for the insulin-like peptide from Leydig cells, RXFP2, previously known as LGR8. The lack of relaxin impairs male fertility but the precise distribution and the function of relaxin receptors in the male reproductive tract is not known. We investigated the distribution of Rxfp1 and Rxfp2 in the reproductive tract of the male rat and the function of relaxin in the vas deferens, a tissue with high expression of both receptors. 相似文献11.
Concordance between genetic relatedness and phenotypic similarities of Trichomonas vaginalis strains
Vladimír Hampl Štěpánka Vaňáčová Jaroslav Kulda Jaroslav Flegr 《BMC evolutionary biology》2001,1(1):11-10
Background
Despite the medical importance of trichomoniasis, little is known about the genetic relatedness of Trichomonas vaginalis strains with similar biological characteristics. Furthermore, the distribution of endobionts such as mycoplasmas or Trichomonas vaginalis virus (TVV) in the T. vaginalis metapopulation is poorly characterised. 相似文献12.
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Christopher G Wilson Eric J Vanderploeg Fengrong Zuo John D Sandy Marc E Levenston 《Arthritis research & therapy》2009,11(6):R173
Introduction
Little is known about endogenous or cytokine-stimulated aggrecan catabolism in the meniscal fibrocartilage of the knee. The objectives of this study were to characterize the structure, distribution, and processing of aggrecan in menisci from immature bovines, and to identify mechanisms of extracellular matrix degradation that lead to changes in the mechanical properties of meniscal fibrocartilage. 相似文献14.
Grégory Nuel 《Algorithms for molecular biology : AMB》2006,1(1):17-13
Background:
In order to compute pattern statistics in computational biology a Markov model is commonly used to take into account the sequence composition. Usually its parameter must be estimated. The aim of this paper is to determine how sensitive these statistics are to parameter estimation, and what are the consequences of this variability on pattern studies (finding the most over-represented words in a genome, the most significant common words to a set of sequences,...). 相似文献15.
Background
The discovery of cis-regulatory motifs still remains a challenging task even though the number of sequenced genomes is constantly growing. Computational analyses using pattern search algorithms have been valuable in phylogenetic footprinting approaches as have expression profile experiments to predict co-occurring motifs. Surprisingly little is known about the nature of cis-regulatory element (CRE) distribution in promoters. 相似文献16.
Background
The cystatin superfamily comprises cysteine protease inhibitors that play key regulatory roles in protein degradation processes. Although they have been the subject of many studies, little is known about their genesis, evolution and functional diversification. Our aim has been to obtain a comprehensive insight into their origin, distribution, diversity, evolution and classification in Eukaryota, Bacteria and Archaea. 相似文献17.
Gregory J Dick Anders F Andersson Brett J Baker Sheri L Simmons Brian C Thomas A Pepper Yelton Jillian F Banfield 《Genome biology》2009,10(8):R85-16
Background
Analyses of DNA sequences from cultivated microorganisms have revealed genome-wide, taxa-specific nucleotide compositional characteristics, referred to as genome signatures. These signatures have far-reaching implications for understanding genome evolution and potential application in classification of metagenomic sequence fragments. However, little is known regarding the distribution of genome signatures in natural microbial communities or the extent to which environmental factors shape them. 相似文献18.
Diffusion tensor imaging and tractwise fractional anisotropy statistics: quantitative analysis in white matter pathology 总被引:1,自引:0,他引:1
Hans-Peter Mueller Alexander Unrath Anne D Sperfeld Albert C Ludolph Axel Riecker Jan Kassubek 《Biomedical engineering online》2007,6(1):42
Background
Information on anatomical connectivity in the brain by measurements of the diffusion of water in white matter tracts lead to quantification of local tract directionality and integrity. 相似文献19.
Background
Tripeptidyl-peptidase I, also known as CLN2, is a member of the family of sedolisins (serine-carboxyl peptidases). In humans, defects in expression of this enzyme lead to a fatal neurodegenerative disease, classical late-infantile neuronal ceroid lipofuscinosis. Similar enzymes have been found in the genomic sequences of several species, but neither systematic analyses of their distribution nor modeling of their structures have been previously attempted. 相似文献20.
Nicole Maca-Meyer Ana M González José M Larruga Carlos Flores Vicente M Cabrera 《BMC genetics》2001,2(1):13-8