共查询到20条相似文献，搜索用时 31 毫秒
1.
Alexey S Kondrashov Inna S Povolotskaya Dmitry N Ivankov Fyodor A Kondrashov 《Biology direct》2010,5(1):5
Background
Divergence of two independently evolving sequences that originated from a common ancestor can be described by two parameters, the asymptotic level of divergence E and the rate r at which this level of divergence is approached. Constant negative selection impedes allele replacements and, therefore, is routinely assumed to decelerate sequence divergence. However, its impact on E and on r has not been formally investigated. 相似文献2.
Background
Comparative sequence analysis is an effective and increasingly common way to identifycis-regulatory regions in animal genomes. 相似文献3.
Background
Complete sequencing and annotation of the 96.2 kb Bacillus anthracis plasmid, pXO2, predicted 85 open reading frames (ORFs). Bacillus cereus and Bacillus thuringiensis isolates that ranged in genomic similarity to B. anthracis, as determined by amplified fragment length polymorphism (AFLP) analysis, were examined by PCR for the presence of sequences similar to 47 pXO2 ORFs. 相似文献4.
Background
The f factor is a new parameter for accommodating the influence of both the starting and ending states in the rate matrices of "generalized weighted frequencies" (+gwF) models for sequence evolution. In this study, we derive an expected value for f, starting from a nearly neutral model of weak selection, and then assess the biological interpretation of this factor with evolutionary simulations. 相似文献5.
Sean R Eddy 《BMC bioinformatics》2002,3(1):18-16
Background
Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N 3) in memory. This is only practical for small RNAs. 相似文献6.
Background
We present a complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous version 2.2 of DIALIGN. This previous version is superior to Needleman-Wunsch-based multi-alignment programs on locally related sequence sets. However, it is often outperformed by these methods on data sets with global but weak similarity at the primary-sequence level. 相似文献7.
8.
Background
In 2004, Bejerano et al. announced the startling discovery of hundreds of "ultraconserved elements", long genomic sequences perfectly conserved across human, mouse, and rat. Their announcement stimulated a flurry of subsequent research. 相似文献9.
Muktak Aklujkar Julia Krushkal Genevieve DiBartolo Alla Lapidus Miriam L Land Derek R Lovley 《BMC microbiology》2009,9(1):109-22
Background
The genome sequence of Geobacter metallireducens is the second to be completed from the metal-respiring genus Geobacter, and is compared in this report to that of Geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and differences. 相似文献10.
Hsiu-Yu Wang Hao-Teng Chang Tun-Wen Pai Chung-I Wu Yuan-Hung Lee Yen-Hsin Chang Hsiu-Ling Tai Chuan-Yi Tang Wei-Yao Chou Margaret Dah-Tsyr Chang 《BMC molecular biology》2007,8(1):89
Background
Human eosinophil-derived neurotoxin (edn) and eosinophil cationic protein (ecp) are members of a subfamily of primate ribonuclease (rnase) genes. Although they are generated by gene duplication event, distinct edn and ecp expression profile in various tissues have been reported. 相似文献11.
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12.
Sònia Casillas Bárbara Negre Antonio Barbadilla Alfredo Ruiz 《BMC evolutionary biology》2006,6(1):106-15
Background
It is expected that genes that are expressed early in development and have a complex expression pattern are under strong purifying selection and thus evolve slowly. Hox genes fulfill these criteria and thus, should have a low evolutionary rate. However, some observations point to a completely different scenario. Hox genes are usually highly conserved inside the homeobox, but very variable outside it. 相似文献13.
Wei Ji Yong Li Jie Li Cui-hong Dai Xi Wang Xi Bai Hua Cai Liang Yang Yan-ming Zhu 《BMC plant biology》2006,6(1):4-7
Background
Salinization causes negative effects on plant productivity and poses an increasingly serious threat to the sustainability of agriculture. Wild soybean (Glycine soja) can survive in highly saline conditions, therefore provides an ideal candidate plant system for salt tolerance gene mining. 相似文献14.
William G Miller Irene V Wesley Stephen LW On Kurt Houf Francis Mégraud Guilin Wang Emma Yee Apichai Srijan Carl J Mason 《BMC microbiology》2009,9(1):196
Background
Arcobacter spp. are a common contaminant of food and water, and some species, primarily A. butzleri and A. cryaerophilus, have been isolated increasingly from human diarrheal stool samples. Here, we describe the first Arcobacter multilocus sequence typing (MLST) method for A. butzleri, A. cryaerophilus, A. skirrowii, A. cibarius and A. thereius. 相似文献15.
16.
Christoph Kaleta Anna Göhler Stefan Schuster Knut Jahreis Reinhard Guthke Swetlana Nikolajewa 《BMC systems biology》2010,4(1):116
Background
Although Escherichia coli is one of the best studied model organisms, a comprehensive understanding of its gene regulation is not yet achieved. There exist many approaches to reconstruct regulatory interaction networks from gene expression experiments. Mutual information based approaches are most useful for large-scale network inference. 相似文献17.
Background
Although the gene encoding for glutamine synthetase (gln A) is essential in several organisms, multiple glnA copies have been identified in bacterial genomes such as those of the phylum Actinobacteria, notably the mycobacterial species. Intriguingly, previous reports have shown that only one copy (gln A1) is essential for growth in M. tuberculosis, while the other copies (gln A2, gln A3 and gln A4) are not. 相似文献18.
Rob Lavigne Paul Darius Elizabeth J Summer Donald Seto Padmanabhan Mahadevan Anders S Nilsson Hans W Ackermann Andrew M Kropinski 《BMC microbiology》2009,9(1):224-16
Background
We advocate unifying classical and genomic classification of bacteriophages by integration of proteomic data and physicochemical parameters. Our previous application of this approach to the entirely sequenced members of the Podoviridae fully supported the current phage classification of the International Committee on Taxonomy of Viruses (ICTV). It appears that horizontal gene transfer generally does not totally obliterate evolutionary relationships between phages. 相似文献19.
Background
Determining beforehand specific positions to align (anchor points) has proved valuable for the accuracy of automated multiple sequence alignment (MSA) software. This feature can be used manually to include biological expertise, or automatically, usually by pairwise similarity searches. Multiple local similarities are be expected to be more adequate, as more biologically relevant. However, even good multiple local similarities can prove incompatible with the ordering of an alignment. 相似文献20.