共查询到20条相似文献,搜索用时 15 毫秒
1.
Shanmuga Sozhamannan Michael D Chute Farrell D McAfee Derrick E Fouts Arya Akmal Darrell R Galloway Alfred Mateczun Leslie W Baillie Timothy D Read 《BMC microbiology》2006,6(1):34-11
Background
Bacillus anthracis is considered to be a recently emerged clone within the Bacillus cereus sensu lato group. The B. anthracis genome sequence contains four putative lambdoid prophages. We undertook this study in order to understand whether the four prophages are unique to B. anthracis and whether they produce active phages. 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.
Kannan Tharakaraman Leonardo Mari?o-Ramírez Sergey L Sheetlin David Landsman John L Spouge 《BMC bioinformatics》2006,7(1):408
Background
Many DNA regulatory elements occur as multiple instances within a target promoter. Gibbs sampling programs for finding DNA regulatory elements de novo can be prohibitively slow in locating all instances of such an element in a sequence set. 相似文献4.
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5.
Mónica Oleastro Rita Cordeiro Armelle Ménard Yoshio Yamaoka Dulciene Queiroz Francis Mégraud Lurdes Monteiro 《BMC microbiology》2009,9(1):248
Background
The homB gene is a Helicobacter pylori disease-marker candidate, strongly associated with peptic ulcer disease, while homA, its paralogue gene with 90% sequence identity, is correlated with non-ulcer dyspepsia. The HomB encoded outer membrane protein was shown to contribute to the proinflammatory properties of H. pylori and also to be involved in bacterial adherence. 相似文献6.
Gordon Blackshields Fabian Sievers Weifeng Shi Andreas Wilm Desmond G Higgins 《Algorithms for molecular biology : AMB》2010,5(1):21
Background
The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences. This requires memory and time proportional to N 2 for N sequences. When N grows larger than 10,000 or so, this becomes increasingly prohibitive and can form a significant barrier to carrying out very large multiple alignments. 相似文献7.
Background
Analysis of the first reported complete genome sequence ofBifidobacterium longumNCC2705, an actinobacterium colonizing the gastrointestinal tract, uncovered its proteomic relatedness toStreptomyces coelicolorandMycobacterium tuberculosis. However, a rapid scrutiny by genometric methods revealed a genome organization totally different from all so far sequenced high-GC Gram-positive chromosomes. 相似文献8.
Adebola AJ Raji James V Anderson Olufisayo A Kolade Chike D Ugwu Alfred GO Dixon Ivan L Ingelbrecht 《BMC plant biology》2009,9(1):118-11
Background
Cassava (Manihot esculenta Crantz), a starchy root crop grown in tropical and subtropical climates, is the sixth most important crop in the world after wheat, rice, maize, potato and barley. The repertoire of simple sequence repeat (SSR) markers for cassava is limited and warrants a need for a larger number of polymorphic SSRs for germplasm characterization and breeding applications. 相似文献9.
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10.
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12.
Background
Extracting motifs from sequences is a mainstay of bioinformatics. We look at the problem of mining structured motifs, which allow variable length gaps between simple motif components. We propose an efficient algorithm, called EXMOTIF, that given some sequence(s), and a structured motif template, extracts all frequent structured motifs that have quorum q. Potential applications of our method include the extraction of single/composite regulatory binding sites in DNA sequences. 相似文献13.
Heike Feldhaar Josef Straka Markus Krischke Kristina Berthold Sascha Stoll Martin J Mueller Roy Gross 《BMC biology》2007,5(1):48
Background
Carpenter ants (genus Camponotus) are considered to be omnivores. Nonetheless, the genome sequence of Blochmannia floridanus, the obligate intracellular endosymbiont of Camponotus floridanus, suggests a function in nutritional upgrading of host resources by the bacterium. Thus, the strongly reduced genome of the endosymbiont retains genes for all subunits of a functional urease, as well as those for biosynthetic pathways for all but one (arginine) of the amino acids essential to the host. 相似文献14.
Background
Trypanosoma brucei is the causative agent of human sleeping sickness and animal trypanosomiasis in sub-Saharan Africa, and it has been subdivided into three subspecies: Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense, which cause sleeping sickness in humans, and the nonhuman infective Trypanosoma brucei brucei. T. b. gambiense is the most clinically relevant subspecies, being responsible for more than 90% of all trypanosomal disease in humans. The genome sequence is now available, and a Mendelian genetic system has been demonstrated in T. brucei, facilitating genetic analysis in this diploid protozoan parasite. As an essential step toward identifying loci that determine important traits in the human-infective subspecies, we report the construction of a high-resolution genetic map of the STIB 386 strain of T. b. gambiense. 相似文献15.
Mark WJ van Passel 《Biology direct》2008,3(1):12
Most sequenced strains from Pasteurellaceae and Neisseriae contain hundreds to thousands of uptake sequence (US) motifs in their genome, which are associated with natural competence for DNA uptake. The mechanism of their recognition is still unclear, and I searched for intragenic location patterns of these motifs for clues about their distribution. In all cases, one orientation of the US has a higher occurrence in the reading frame, and in all Pasteurellaceae, the US and the reverse complement motifs are biased towards the gene termini. These findings could help design experimental set-ups to study preferential DNA uptake, thereby further unravelling the phenomenon of natural competence. 相似文献
16.
Background
A new algorithm has been developed for generating conservation profiles that reflect the evolutionary history of the subfamily associated with a query sequence. It is based on n-gram patterns (NP{n,m}) which are sets of n residues and m wildcards in windows of size n+m. The generation of conservation profiles is treated as a signal-to-noise problem where the signal is the count of n-gram patterns in target sequences that are similar to the query sequence and the noise is the count over all target sequences. The signal is differentiated from the noise by applying singular value decomposition to sets of target sequences rank ordered by similarity with respect to the query. 相似文献17.
Anne Roulin Benoit Piegu Philippe M Fortune Fran?ois Sabot Angélique D'Hont Domenica Manicacci Olivier Panaud 《BMC evolutionary biology》2009,9(1):58
Background
Horizontal transfers (HTs) refer to the transmission of genetic material between phylogenetically distant species. Although most of the cases of HTs described so far concern genes, there is increasing evidence that some involve transposable elements (TEs) in Eukaryotes. The availability of the full genome sequence of two cereal species, (i.e. rice and Sorghum), as well as the partial genome sequence of maize, provides the opportunity to carry out genome-wide searches for TE-HTs in Poaceae. 相似文献18.
19.
Delineating the structural,functional and evolutionary relationships of sucrose phosphate synthase gene family II in wheat and related grasses 总被引:1,自引:0,他引:1
Shailendra Sharma Nese Sreenivasulu Vokkaliga Thammegowda Harshavardhan Christiane Seiler Shiveta Sharma Zaynali Nezhad Khalil Eduard Akhunov Sunish Kumar Sehgal Marion S Röder 《BMC plant biology》2010,10(1):134
Background
Sucrose phosphate synthase (SPS) is an important component of the plant sucrose biosynthesis pathway. In the monocotyledonous Poaceae, five SPS genes have been identified. Here we present a detailed analysis of the wheat SPSII family in wheat. A set of homoeologue-specific primers was developed in order to permit both the detection of sequence variation, and the dissection of the individual contribution of each homoeologue to the global expression of SPSII. 相似文献20.