• genome
  • Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H et al (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. (springer.com)
  • In a departure from initial plans , Harvard Medical School's Personal Genome Project will choose participants for whole-genome sequencing based on their phenotype, according to project organizers. (genomeweb.com)
  • Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. (mdpi.com)
  • Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. (mdpi.com)
  • The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence. (mdpi.com)
  • Through studies of gene and especially genome sequences the molecular basis for this diversity can be determined. (pubmedcentralcanada.ca)
  • Evident from genome sequencing are examples of versatile metabolism that go far beyond the canonical pathways described for eukaryotes in textbooks. (pubmedcentralcanada.ca)
  • In the last 2-3 years, genome sequencing and transcript profiling has unveiled several examples of heterotrophic and phototrophic protists that are unexpectedly well-equipped for ATP production using a facultative anaerobic metabolism, including some protists that can ( Chlamydomonas reinhardtii ) or are predicted ( Naegleria gruberi , Acanthamoeba castellanii , Amoebidium parasiticum ) to produce H 2 in their metabolism. (pubmedcentralcanada.ca)
  • Access to whole cancer genome sequencing is important to cancer (or cancer genome) research because: Mutations are the immediate cause of cancer and define the tumor phenotype. (wikipedia.org)
  • Access to methylation profiling is important to cancer research because: Epi-drivers, along with Mut-drivers, can act as immediate causes of cancers Cancer epimutations are cumulative and sometimes related to disease stage The first cancer genome was sequenced in 2008. (wikipedia.org)
  • This study sequenced a typical acute myeloid leukaemia (AML) genome and its normal counterpart genome obtained from the same patient. (wikipedia.org)
  • This analysis validated the approach of whole cancer genome sequencing in identifying somatic mutations and the importance of parallel sequencing of normal and tumor cell genomes. (wikipedia.org)
  • In 2011, the genome of an exceptional bladder cancer patient whose tumor had been eliminated by the drug everolimus was sequenced, revealing mutations in two genes, TSC1 and NF2. (wikipedia.org)
  • Because cytosine / guanine base-pairing is generally stronger than adenine / thymine base-pairing, the amount of cytosine and guanine in a genome (called the "GC content") can be estimated by measuring the temperature at which the genomic DNA melts. (wikipedia.org)
  • At present, it is still a long and expensive process to sequence the entire DNA of an organism (its genome). (wikipedia.org)
  • In August 2011, the company expanded its recruiting process by offering an incentive of $20,000 plus a full genome sequence to employees who referred a software engineer. (wikipedia.org)
  • In October 2013, the company announced a collaboration with the Human Genome Sequencing Center at Baylor College of Medicine. (wikipedia.org)
  • genomes
  • The desire to sequence DNA is fueled by the knowledge that the information locked inside of genomes can help fields as varied as molecular medicine, bioarcheology, forensics, and environmental science. (nsti.org)
  • The number of sequenced nuclear genomes of protists is small, even when considered against the small fraction of protist biodiversity that has been morphologically described. (pubmedcentralcanada.ca)
  • The initiative allows such exceptional patients (who have responded positively for at least six months to a cancer drug that usually fails) to have their genomes sequenced to identify the relevant mutations. (wikipedia.org)
  • Through the partnership, DNAnexus and scientists at Baylor performed the largest cloud-based genomics analysis to date, processing 3,751 whole human genomes and 10,771 exomes. (wikipedia.org)
  • Molecules
  • Method for rapid-base sequencing in DNA and RNA with two-base labeling and employing fluorescent detection of single molecules at two wavelengths. (patents.com)
  • High-Speed DNA Sequencing: An Approach Based Upon Fluorescence Detection of Single Molecules," J. Biomolecular Struc. (patents.com)
  • Strand separation by gentle heating, as used in PCR, is simple providing the molecules have fewer than about 10,000 base pairs (10 kilobase pairs, or 10 kbp). (wikipedia.org)
  • Hybrid molecules are formed between similar sequences and any differences between those sequences will result in a disruption of the base-pairing. (wikipedia.org)
  • A comprehensive step-by-step protocol on constructing phylogenetic tree, including DNA/Amino Acid contiguous sequence assembly, multiple sequence alignment, model-test (testing best-fitting substitution models) and phylogeny reconstruction using Maximum Likelihood and Bayesian Inference, is available at Nature Protocol Early attempts at molecular systematics were also termed as chemotaxonomy and made use of proteins, enzymes, carbohydrates, and other molecules that were separated and characterized using techniques such as chromatography. (wikipedia.org)
  • Morpholinos block access of other molecules to small (~25 base) specific sequences of the base-pairing surfaces of ribonucleic acid (RNA). (wikipedia.org)
  • Instead, Morpholinos act by "steric blocking", binding to a target sequence within an RNA, inhibiting molecules that might otherwise interact with the RNA. (wikipedia.org)
  • genetic
  • Boston-based startup Good Start Genetics has raised $18 million in a Series A financing round for the development and launch of its sequencing-based pre-pregnancy genetic screening test, the company said last week. (genomeweb.com)
  • In general, these are considered superior for evolutionary studies, since the actions of evolution are ultimately reflected in the genetic sequences. (wikipedia.org)
  • homology
  • In 1999, working with John Carlson at Yale, he developed a novel algorithm for computationally identifying G Protein-Coupled Receptors (GPCR) without using primary sequence homology, which led to the cloning of olfactory receptors in insects. (wikipedia.org)
  • examined misidentification of VGS submitted to antimicrobial surveillance programs as pneumococci and found that the distinction of S. pneumoniae from the VGS can be difficult, which is not surprising in light of the fact that S. mitis and S. oralis possess >99% sequence homology with S. pneumoniae (47). (wikipedia.org)
  • mutations
  • The remaining 8 were new mutations and all were single base changes: Four were in families that are strongly associated with cancer pathogenesis (PTPRT, CDH24, PCLKC and SLC15A1). (wikipedia.org)
  • restriction
  • citation needed] While a postdoctoral fellow with Hamilton O. Smith at the Johns Hopkins University School of Medicine during 1969-70, Kelly determined the DNA sequences recognized by type II restriction enzymes, which subsequently became major tools in recombinant DNA research. (wikipedia.org)
  • The underlying assumption is that each microbe in the sample will have a different sequence on the target gene, so a restriction enzyme will cut each microbe's DNA in a different place. (wikipedia.org)
  • detect
  • DNA denaturation can also be used to detect sequence differences between two different DNA sequences. (wikipedia.org)
  • In the context of a single isolated region of DNA, denaturing gradient gels and temperature gradient gels can be used to detect the presence of small mismatches between two sequences, a process known as temperature gradient gel electrophoresis. (wikipedia.org)
  • canonical
  • In the canonical Watson-Crick base pairing, adenine (A) forms a base pair with thymine (T) and guanine (G) forms one with cytosine (C) in DNA. (wikipedia.org)
  • Examples include universal bases, which can pair with all four canonical bases, and phosphate-sugar backbone analogues such as PNA, which affect the properties of the chain (PNA can even form a triple helix). (wikipedia.org)
  • The viral polymerase incorporates these compounds with non-canonical bases. (wikipedia.org)
  • These nucleoside triphosphates possess a non-canonical sugar, dideoxyribose, which lacks the 3' hydroxyl group normally present in DNA and therefore cannot bond with the next base. (wikipedia.org)
  • analysis
  • we would like to do some sequence analysis with the students. (bioinformatics.org)
  • This webinar will highlight a comprehensive end-to-end solution for precision care in oncology, comprising sample acquisition through to sequencing and analysis, treatment recommendations, and follow-through. (genomeweb.com)
  • DNAnexus is an American company that provides a cloud-based data analysis and management platform for DNA sequence data. (wikipedia.org)
  • DNAnexus was founded in early 2009 as a spin-off from Stanford University to address the need for computing infrastructure in DNA sequence analysis. (wikipedia.org)
  • Customers of DNAnexus use those computational resources to run analysis programs on DNA sequence data and to store that data. (wikipedia.org)
  • In September 2013, the company began offering its cloud-based platform-as-a-service to clinical testing laboratories for DNA sequence data analysis. (wikipedia.org)
  • DNAnexus Aims to Alleviate Next-Gen Sequence Analysis Headache with Cloud-based Service. (wikipedia.org)
  • http://www.genomeweb.com/sequencing/dnanexus-aims-alleviate-next-gen-sequence-analysis-headache-cloud-based-service Ricketts, Camille. (wikipedia.org)
  • http://www.fiercebiotechit.com/special-reports/fierce-s-top-10-biotech-techies/andreas-sundquist-fierces-top-10-biotech-techies http://genengnews.com/gen-news-highlights/baylor-39-s-hgsc-dnanexus-amazon-team-up-in-cloud-based-analysis/81249025/?kwrd=dnanexus Grens, Kerry. (wikipedia.org)
  • Gene Expression
  • For addressing the needs of modeling, simulation and visualization of large and diverse biological datasets from sequence, gene expression and proteomics datasets, "systems biology" (Hood 2003) approaches are being developed for construction of gene regulatory networks (Dojer et al. (springer.com)
  • wobble
  • In RNA, thymine is replaced by uracil (U). Alternate hydrogen bonding patterns, such as the wobble base pair and Hoogsteen base pair, also occur-particularly in RNA-giving rise to complex and functional tertiary structures. (wikipedia.org)
  • The GU wobble base pair, with two hydrogen bonds, does occur fairly often in RNA. (wikipedia.org)
  • The first anticodon base, or wobble-position, is sometimes modified to inosine (derived from adenine), pseudouridine or lysidine (derived from cytosine). (wikipedia.org)
  • Some anticodons can pair with more than one codon due to a phenomenon known as wobble base pairing. (wikipedia.org)
  • strands
  • DNA denaturation, also called DNA melting, is the process by which double-stranded deoxyribonucleic acid unwinds and separates into single-stranded strands through the breaking of hydrophobic stacking attractions between the bases. (wikipedia.org)
  • cleavage
  • The bases are then sequentially cleaved from the replicated strand, excited with a chosen spectrum of electromagnetic radiation, and the fluorescence from individual, tagged bases detected in the order of cleavage from the strand. (patents.com)
  • EcoRII is a bacterial Type IIE REase that interacts with two or three copies of the pseudopalindromic DNA recognition sequence 5'-CCWGG-3' (W = A or T), one being the actual target of cleavage, the other(s) serving as the allosteric activator(s). (wikipedia.org)
  • representation
  • DNA samples from two groups of Italian Large White pigs with divergent estimating breeding value (EBV) for BFT were separately pooled and sequenced, after preparation of reduced representation libraries (RRLs), on the Ion Torrent technology. (hindawi.com)
  • Methodology
  • For building the optimized test schedule, frequency based pseudo damage methodology called Relative Damage Spectrum (RDS) is incorporated.This method enhances the proving ground durability validation process by providing optimized test schedules to prevent redundant vehicle testing. (sae.org)
  • typical
  • they also lack either the polysaccharide-based capsule typical of S. pneumoniae or the Lancefield antigens of the pyogenic members of the genus. (wikipedia.org)
  • optimal
  • Hence the PG test sequence must be optimal enough such that it includes all the range of frequencies representing the actual customer load spectra. (sae.org)
  • De Bona F, Ossowski S, Schneeberger K, Ratsch G (2008) Optimal spliced alignments of short sequence reads. (springer.com)
  • specific
  • PG validation requires a specific durability test sequence for every segment of commercial vehicles due to different customer usage applications and terrain conditions. (sae.org)
  • A modified S-SAP (sequence-specific amplified polymorphism) method with universal primers for retrotransposons was used to study Vitis vinifera cv. (ajevonline.org)
  • Stem
  • The T arm is a 4- to 5- bp stem containing the sequence TΨC where Ψ is pseudouridine, a modified uridine. (wikipedia.org)
  • different
  • The secondary structures of biological DNA's and RNA's tend to be different: biological DNA mostly exists as fully base paired double helices, while biological RNA is single stranded and often forms complex and intricate base-pairing interactions due to its increased ability to form hydrogen bonds stemming from the extra hydroxyl group in the ribose sugar. (wikipedia.org)
  • Typically the analogue nucleobases confer, among other things, different base pairing and base stacking properties. (wikipedia.org)
  • single
  • Bases modified to accept fluorescent labels are used to replicate a single DNA or RNA strand to be sequenced. (patents.com)
  • a substantial sample of individuals of the target species or other taxon is used, however many current studies are based on single individuals. (wikipedia.org)
  • pair
  • For each base pair, considered relative to its predecessor, there are the following base pair geometries to consider: Shear Stretch Stagger Buckle Propeller: rotation of one base with respect to the other in the same base pair. (wikipedia.org)
  • Opening Shift: displacement along an axis in the base-pair plane perpendicular to the first, directed from the minor to the major groove. (wikipedia.org)
  • Slide: displacement along an axis in the plane of the base pair directed from one strand to the other. (wikipedia.org)
  • Note that "tilt" has often been used differently in the scientific literature, referring to the deviation of the first, inter-strand base-pair axis from perpendicularity to the helix axis. (wikipedia.org)