sequencing contig assembly and gene annotation
Báo cáo y học: "BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources" doc
... http://www.ensembl.org/Homo_sapiens/geneview ?gene= {{EnsemblGene}} Entrez Gene (NCBI) http://www.ncbi.nlm.nih.gov/sites/entrez?db =gene& cmd=retrieve&list_uids={{EntrezGene}} Gene Cards http://www.genecards.org/cgi-bin/carddisp.pl?id_type=entrezgene&id= ... search interface, which accepts most public gene identifiers (Entrez Gene, Ensembl, Refseq, Uniprot, Affymetrix, and so on) and gene annotation identifiers (Gene Ontology, Interpro), as well as coordinates ... a gene out of the search result list displays a gene annotation report In the case of BioGPS, the default gene annotation report focuses on our reference 'Gene Atlas' data sets, which show gene...
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báo cáo khoa học: "EST sequencing and gene expression profiling of defence-related genes from Persea americana infected with Phytophthora cinnamomi" pot
... ranging from general defence-related genes (metallothioneins, thaumatin and universal stress genes) to more specific oomycete defence-related genes (pathogenesis related protein PR10 and the oxysterolbinding ... ribosomal structure and biogenesis; signal transduction mechanisms and general function prediction contained a combined total of 34.8% of all contigs According to the GO database the Table Contig classification ... protein, metallothionein and thaumatin-like genes as well as cytochrome P450) and Phytophthora specific response genes such as (thaumatin, PR-10 and the LRR resistance protein-like gene) [44-47,49-52,55,64]...
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Báo cáo y học: "Molecular processes during fat cell development revealed by gene expression profiling and functional annotation" pptx
... lipogenesis and adipogenesis ADD1/SREBP1c can activate a broad program of genes that are involved in fatty acid and triglyceride metabolism in both fat and liver, and can also accelerate adipogenesis ... discovered fat cell gene products, and candidate transcription factors expressed during adipogenesis The numbering of the genes is given according to the de novo functional annotation (Additional ... many genes and that one gene can be regulated by a number of miRNAs The function of the potential target genes was diverse and included transcription factors, enzymes, transmembrane proteins, and...
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Towards automatic gene synthesis with bioinformatics software, novel one step real time PCR assembly, and lab chip gene synthesis 1
... understanding of genes synthesis, the shortcomings or limitation of various synthesis schemes and appreciations on the complexity of current genes synthesis methods 1.1 Overview gene synthesis In general, ... gene synthesis is developed, which combines the gene assembly and gene amplifications into a single PCR step To our knowledge, Page National University of Singapore Department of Electrical and ... the generation of specific restriction site to prevent mis-hybridization during gene assembly process Designed and implemented a gene synthesis model that allows the systematic analysis and studies...
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Towards automatic gene synthesis with bioinformatics software, novel one step real time PCR assembly, and lab chip gene synthesis 2
... of the assembly mixture will increase the half-life in gene assembly The outer primer and assembly oligonucleotide have Page 69 National University of Singapore Department of Electrical and Computer ... integrated two-step gene synthesis chip 6.3.1 Gene assembly and amplification Published sequence of GFPuv gene segment with a total length of 760 bp (sequence 261-1020 with T357C, T811A and C812G base ... handling time and reagents costs, and eliminate human process factors Page 98 National University of Singapore Department of Electrical and Computer Engineering PCR product cloning and DNA sequencing...
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Paired end transcriptome assembly and genomic variants management for next generation sequencing data
... Next Generation Sequencing Maxam-Gilbert sequencing and Sanger sequencing (28) are called first generation sequencing technologies Although they are introduced at the same time, Sanger sequencing ... efficient method for gene discovery and remains the gold standard for annotation of both coding and noncoding genes (16) There are mainly two categories of technologies to deduce and quantify the ... Nowadays, transcriptome assembly generally follows the development of genome assembly, in which coverage information is widely and reliably used for contig extension, error detection and correction However,...
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Self-Assembly and Nanotechnology: A Force Balance Approach
... IMPLICATIONS OF SELF -ASSEMBLY FOR NANOTECHNOLOGY 8.1 General Concepts and Approach to Nanotechnology 8.2 Self -Assembly and Nanotechnology Share the Same Building Units 8.3 Self -Assembly and Nanotechnology ... APPROACH TO SELF -ASSEMBLY UA,P(x) and UR,P(x) represent the attractive and repulsive potentials for the selfassembly of primary building units, respectively UA,S(x) and UR,S(x), and UA,T(x) and UR,T(x) ... Preface and Acknowledgments PART I SELF -ASSEMBLY xv UNIFIED APPROACH TO SELF -ASSEMBLY 1.1 Self -Assembly through Force Balance 1.2 General Scheme for the Formation of Self-Assembled Aggregates 1.3 General...
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The 8051 microcontroller and embedded systems using assembly and c 2nd ed
... Logic Instructions And Programs 8051 Programming in C 8051 Hardware Connection and Hex File 8051 Timer/Counter Programming in Assembly and C 8051 Serial Port Programming in Assembly and C Interrupts ... Microcontroller and Embedded Systems: Using Assembly and C Mazidi, Mazidi and McKinlay Chung-Ping Young 楊中平 Home Automation, Networking, and Entertainment Lab Dept of Computer Science and Information ... Microcontroller and Embedded Systems: Using Assembly and C Mazidi, Mazidi and McKinlay Chung-Ping Young 楊中平 Home Automation, Networking, and Entertainment Lab Dept of Computer Science and Information...
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Tài liệu Báo cáo khoa học: Novel aspects of heat shock factors: DNA recognition, chromatin modulation and gene expression ppt
... Sakurai and Y Enoki SWI ⁄ SNF complexes are recruited to both the promoter and coding regions, and histones are acetylated and displaced [56–58] However, the presence of SAGA and SWI ⁄ SNF, and a ... of the chicken HSF3 gene; however, the human HSF3 gene is a pseudogene [41] Mouse HSF3 translocates into the nucleus upon heat shock and may activate nonclassical heat shock genes, but does not ... localizes in the nucleus and binds to and regulates basal expression via HSEs of target genes [26] Deletion of the HSF gene is lethal to cells, even at physiological temperatures The genes targeted by...
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Tài liệu Báo cáo khoa học: Time-dependent regulation analysis dissects shifts between metabolic and gene-expression regulation during nitrogen starvation in baker’s yeast doc
... of gene expression of a certain gene (X) normalized to the mean of the control gene PDI1 and the steady-state sample of the chemostat culture (Eqns and 7) We have normalized to steady state and ... Netherlands), pmol of each primer (Isogen, De Meern, The Netherlands or Biolegio, Nijmegen, The Netherlands) and lL of cDNA template (equivalent to ng of RNA) Amplification, data acquisition, and ... substrates, products and effectors (X), and by changes in the affinities (1 ⁄ K) of enzyme e towards its substrates, products and effectors (K) As derived previously [6,7], gene expression and metabolic...
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Tài liệu Báo cáo khoa học: Tryptophan tryptophylquinone cofactor biogenesis in the aromatic amine dehydrogenase of Alcaligenes faecalis Cofactor assembly and catalytic properties of recombinant enzyme expressed in Paracoccus denitrificans pptx
... orf-4 and hemE) all putatively transcribed in the same direction [7] The second and fifth genes (aauA and aauB) encode the large and small subunits of AADH, respectively The genes aauD and aauE ... Science 252, 817–824 Chistoserdov AY (2001) Cloning, sequencing and mutagenesis of the genes for aromatic amine dehydrogenase from Alcaligenes faecalis and evolution of amine dehydrogenases Microbiology ... 0.02 ± ± ± ± 0.01 0.01 0.01 0.02 mauM and mauN genes, but analogues for these genes are not found around the aauBEDA gene cluster [7] We have shown that TTQ biogenesis in recombinant AADH is functional...
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Tài liệu Báo cáo khoa học: "Demonstration of the UAM CorpusTool for text and image annotation" docx
... Figure 4: Annotation Storage Example 14 This window allows the user to add new annotation layers to the project, and edit/extend the annotation scheme for each layer (by ... can swipe regions of the image to create a selection, and assign features to the selection Since stand-off annotation is used for both text and image, much of the code-base is common between the ... creating and editing the coding scheme (the tag set) UAM CorpusTool uses a hierarchally organised tag scheme, allowing crossclassification and multiple inheritance (both disjunctive and conjunctive)...
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Báo cáo khoa học: Assembly and molecular mode of action of the Helicobacter pylori Cag type IV secretion apparatus doc
... duplication of cagA and cagB associated with cagA degeneration, and a more complex rearrangement comprising all cag genes except cagA and a second inversion of several flanking genes (green) Examples ... repeat-containing protein and gene hp0549 encoding glutamate racemase Gene designations and putative homologies to components of the A tumefaciens T-DNA transfer system are indicated The left (LJ) and right ... type IV secretion apparatus Gene arrangement and variants of the cagPAI The cagPAI, which was originally identified by sequencing the genome region upstream of the cagA gene or DNA found only in...
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Ambient particulate air pollution induces oxidative stress and alterations of mitochondria and gene expression in brown and white adipose tissues ppt
... and a regression to a WAT phenotype [decrease in BAT specific genes (Pgc-1a, Dio2, Ucp1) and increase in WAT-specific genes (Hoxc9 and Igfbp3)] This shift was not seen in WAT, when the same genes ... oxidative stress and alterations of mitochondria and gene expression in brown and white adipose tissues Particle and Fibre Toxicology 2011 8:20 Submit your next manuscript to BioMed Central and take ... lesions on a standard chow diet It is used for studies of hyperlipidemia and atherosclerosis, and has been used extensively in understanding the mechanisms of lipoprotein metabolism and atherosclerosis...
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Báo cáo khoa học: Nuclear actin and actin-binding proteins in the regulation of transcription and gene expression docx
... and hnRNP U Moreover, it has been shown that actin, hnRNP U and PCAF associate with the Ser2 ⁄ 5and Ser2-phosphorylated Pol II C-terminal domain hnRNP U and PCAF are present at the promoter and ... as the Nu4A and TIP60 complexes, and INO80 complexes b-Actin is an integral component of chromatin-remodeling complexes, such as the BAF, BAP and INO80 complexes, as well as Nu4A and TIP60 complexes ... activation and actin polymerization [55] Recently, MRTF-A and -B were shown to serve as a link between STARS and SRF In NIH 3T3 cells cotransfected with expression plasmids encoding MRTFs and STARS,...
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Báo cáo khoa học: Molecular characterization and gene disruption of mouse lysosomal putative serine carboxypeptidase 1 ppt
... cell lysates (C) and 50 lL of medium (M) of HT1080 and HT1080-Scpep1 were separated by SDS-PAGE, blotted and probed with the a-His antibody and the a-Scpep1 antisera from rabbit and rat, respectively ... insight into the physiological and cellular function of the putative lysosomal SC Scpep1, we analysed the molecular properties of Scpep1 and generated an Scpep1 gene trap (Scpep1-gt) mouse model ... high transcript levels in kidney and aorta in rat and lower levels in heart, spleen and lung, whereas the human transcript was detected strongly in the kidney and heart but at a low level in a...
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Báo cáo khoa học: The Vps4 C-terminal helix is a critical determinant for assembly and ATPase activity and has elements conserved in other members of the meiotic clade of AAA ATPases pdf
... USA) and rabbit polyclonal anti-(carboxypeptidase Y) and anti-calmodulin sera were gifts from H Riezman (University of Geneva, Switzerland) PCR primers used for plasmid constructions were from GeneWorks ... ATPase domain and C-terminal helix [36] showing the location of residues that were mutated The TRP, RDF and DEL sequences are shown in green, dark blue and red, respectively The b domain and C-terminal ... wild-type Vps4p and inhibit its function in vivo One possible explanation for the difference between our in vivo and in vitro findings is that in vivo Vta1p may allow assembly of otherwise assembly- incompetent...
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Báo cáo khoa học: The 2-oxoacid dehydrogenase multi-enzyme complex of the archaeon Thermoplasma acidophilum ) recombinant expression, assembly and characterization docx
... E2, and NheI ⁄ EcoRI digestion for E3, and purified by gel electrophoresis and gel extraction as already described E2 and E3 genes were separately ligated into the vectors using T4 DNA ligase, generating ... using primers that engineered restriction sites into the 5¢- and 3¢ ends of the gene products: NdeI and XhoI for the E2 gene, and NheI and EcoRI for E3 Oligonucleotides were as follows (restriction ... found an additional gene cluster in H volcanii comprising three genes that would appear to code for OADHC E1a and E1b subunits, and an unattached lipoyl domain; however, no genes for a complete...
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Báo cáo khoa học: Cellular retinol-binding protein type II (CRBPII) in adult zebrafish (Danio rerio) cDNA sequence, tissue-specific expression and gene linkage analysis pptx
... to Gln109 and Gln129 in CRBPI and CRBPII While all FABPs and CRBPs studied to date have the same tertiary structure, the amino-acid residues at positions 109 and 129 may determine ligand-binding ... ancestral CRBP gene that gave rise to the CRBPI and CRBPII genes most likely occurred before the divergence of the teleost fishes and mammals, approximately 400 mya We have shown that the CRBPI gene exists ... data) The mammalian CRBPI and CRBPII genes are linked on chromosome in mouse and in humans and share sequence similarity including the conserved Gln residues at positions 109 and 129 [25,26] Radiation...
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