• detect
  • The results of the parallel analyses are then used to detect common molecular characteristics of the genetic disorder type, which can subsequently be used in the diagnosis or treatment of the disease. (google.com)
  • This method may also be adapted to detect DNA methylation differences, as seen in Methylation-Sensitive Representational Difference Analysis (MS-RDA). (wikipedia.org)
  • To address these challenges, we have previously developed and validated a pan-viral microarray platform called the Virochip with the capacity to detect all known viruses as well as novel variants on the basis of conserved sequence homology 1 . (jove.com)
  • For known exRNA nucleotide sequences, RT-PCR can be applied to detect their presence within a sample as well as quantify their abundance. (wikipedia.org)
  • Here, we use our study to illustrate the use of Exon Arrays to detect alternative isoforms, to outline the analysis involved, and to point out potential problems that may be encountered by researchers using this technology. (igi-global.com)
  • The method of sequencing cDNA to find transcribed genes also runs into problems, such as failing to detect rare or very short RNA molecules, and so do not detect genes that are active only in response to signals or specific to a time frame. (wikipedia.org)
  • loci
  • We have interrogated the transcribed loci in 420 selected ENCyclopedia Of DNA Elements (ENCODE) regions using rapid amplification of cDNA ends (RACE) sequencing. (biomedcentral.com)
  • Such processes have been suggested to be at least partly responsible for mammalian complexity, which is otherwise difficult to explain in view of our relatively low number of genomic loci - less than 25,000 genes in humans, versus approximately 20,000 in the nematode worm C. elegans (Claverie, 2001). (igi-global.com)
  • Virtual karyotype is the digital information reflecting a karyotype, resulting from the analysis of short sequences of DNA from specific loci all over the genome, which are isolated and enumerated. (wikipedia.org)
  • gene expression
  • The gene expression profiles of schistosomes from these animals were obtained and compared by genome-wide oligonucleotide microarray analysis. (paperity.org)
  • The model uses two standardized indices, the standard effect size score for experiments with two groups of data, and a new standardized index that measures the difference in gene expression between treatment and control groups for one sample data with replicate arrays. (nih.gov)
  • Gene expression analysis following host-bacterial interactions is revolutionizing our understanding of the host response to bacterial infection. (bio-medicine.org)
  • Techniques include DNA microarray technology or sequenced-based techniques such as serial analysis of gene expression (SAGE). (wikipedia.org)
  • Due to lowering costs, RNA-Sequencing is becoming more common as a method for cancer gene expression profiling. (wikipedia.org)
  • The process of measuring gene expression via cDNA is called expression analysis or expression profiling. (wikipedia.org)
  • Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, genome-wide association studies, the modeling of evolution and cell division/mitosis. (wikipedia.org)
  • Transcriptomic analysis has enabled the study of how gene expression changes in different organisms and has been instrumental in the understanding of human disease. (wikipedia.org)
  • An analysis of gene expression in its entirety allows detection of broad coordinated trends which cannot be discerned by more targeted assays. (wikipedia.org)
  • In 1995, one of the earliest sequencing-based transcriptomic methods was developed, Serial Analysis of Gene Expression (SAGE), which worked by Sanger sequencing of concatenated random transcript fragments. (wikipedia.org)
  • Although such arrays are perfectly suited to study gene expression profiles, they have limited importance in ChIP experiments since most "interesting" proteins with respect to this technique bind in intergenic regions. (wikipedia.org)
  • molecular
  • A method is disclosed for rapid molecular profiling of tissue or other cellular specimens by placing a donor specimen in an assigned location in a recipient array, providing copies of the array, and performing a different biological analysis of each copy. (google.com)
  • These integrated genomic and molecular studies provide evidence that the IGF1R pathway is a potential therapeutic target for patients with MPNST. (aacrjournals.org)
  • This information deficit is caused by several constraining factors such as the lack of the complete genomic information or the unavailability of molecular tools, for instance, species-specific antibodies. (hindawi.com)
  • Computers became essential in molecular biology when protein sequences became available after Frederick Sanger determined the sequence of insulin in the early 1950s. (wikipedia.org)
  • Dayhoff compiled one of the first protein sequence databases, initially published as books and pioneered methods of sequence alignment and molecular evolution. (wikipedia.org)
  • Some of its major applications include genomics, proteomics, molecular diagnostics, point-of-care diagnostics, tissue engineering, single cell analysis and implantable microdevices. (wikipedia.org)
  • transcripts
  • Gene set enrichment analysis (GSEA) revealed that several of the transcripts encoded transporters associated with the endomembrane system, especially zinc transport. (biomedcentral.com)
  • further analysis suggests that many of the antisense transcripts (but not all) may be artifacts generated from the reverse transcription reaction. (biomedcentral.com)
  • In the 1980s, low-throughput sequencing using the Sanger method was used to sequence random transcripts, producing Expressed Sequence Tags (ESTs). (wikipedia.org)
  • Amounts of individual transcripts were quantified using Northern blotting, nylon membrane arrays, and later Reverse Transcriptase quantitative PCR (RT-qPCR) methods, but these methods are laborious and can only capture a tiny subsection of a transcriptome. (wikipedia.org)
  • So if there are 50 copies of a specific transcript in the biological sample, these transcripts will be captured onto 50 different microbeads, each bead holding roughly 100,000 amplified copies of the specific signature sequence. (wikipedia.org)
  • Traditional methods of gene prediction for annotation of genomic sequences have had problems when used to map the transcriptome, such as not producing an accurate structure of the genes and also missing transcripts entirely. (wikipedia.org)
  • Proteomic
  • Brief Funct Genomic Proteomic. (wikipedia.org)
  • Degradomics is a sub-discipline of biology encompassing all the genomic and proteomic approaches devoted to the study of proteases, their inhibitors, and their substrates on a system-wide scale. (wikipedia.org)
  • encodes
  • The cynS gene that encodes cyanase was identified among bacterial, fungal, and plant sequences in public databases, and the gene was particularly prevalent among cyanobacteria, including numerous Prochlorococcus and Synechococcus strains. (embl-heidelberg.de)
  • quantification
  • The principle of these methods is the identification and quantification of up to ten thousands of RNA and proteins species in a tissue, in contrast to the sequential analysis of conventional methods such as PCR and Western blotting. (hindawi.com)
  • Traditional analytical tools for quantification of DNA, RNA, or proteins are restricted to the sequential analysis of one biomolecule specimen at a time. (hindawi.com)
  • The microbeads are then arrayed in a flow cell for sequencing and quantification. (wikipedia.org)
  • In addition to detecting previously unidentified genes and regulatory sequences, improved quantification of transcription products is possible. (wikipedia.org)
  • transcriptomes
  • However, because no method has existed to isolate bacterial RNA away from host cell RNA, the corresponding analyses of bacterial transcriptomes has been impossible. (bio-medicine.org)
  • In 2008, two human transcriptomes, composed of millions of transcript-derived sequences covering 16,000 genes, were published and, by 2015, transcriptomes had been published for hundreds of individuals. (wikipedia.org)
  • fragments
  • Since driver and tester sequences are nearly identical, the excess of driver DNA fragments will anneal to homologous DNA fragments from the tester species. (wikipedia.org)
  • As more cycles of RDA are performed, the pool of unique sequence fragment copies will grow faster than fragments found in both species. (wikipedia.org)
  • organism's
  • In a particular type of cell or tissue, only a small subset of an organism's genomic DNA will be expressed as mRNAs at any given time. (wikipedia.org)
  • single-stranded
  • Previous research has shown that the fluorescence efficiency of Cy3 and Cy5, covalently attached to the 5' end of single-stranded DNA, is strongly sequence dependent. (jove.com)
  • One concern is that these studies often use reverse transcription to create single-stranded cDNA, but this may also cause second strand synthesis. (biomedcentral.com)
  • Illumina
  • The toolkit comprises user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. (wikipedia.org)
  • proteins
  • This systems analysis revealed that E. coli B is well-suited for production of recombinant proteins due to a greater capacity for amino acid biosynthesis, fewer proteases, and lack of flagella. (biomedcentral.com)
  • We have determined genome sequences of B strains [ 5 , 6 ] - REL606, which has been applied to the study of long-term experimental evolution, and BL21(DE3), which has been used as a cell-factory for overproducing recombinant proteins, biofuels, and a variety of bioproducts on an industrial scale. (biomedcentral.com)
  • Other proteins allow the identification of promoter regions, enhancers, repressors and silencing elements, insulators, boundary elements, and sequences that control DNA replication. (wikipedia.org)
  • DNA sequencing is also the most efficient way to sequence RNA or proteins (via their open reading frames). (wikipedia.org)
  • In eukaryotes, transcription is performed by three types of RNA polymerases, each of which needs a special DNA sequence called the promoter and a set of DNA-binding proteins-transcription factors-to initiate the process. (wikipedia.org)
  • organisms
  • Since DNA is an informative macromolecule in terms of transmission from one generation to another, DNA sequencing is used in evolutionary biology to study how different organisms are related and how they evolved. (wikipedia.org)
  • species
  • When the two species are mixed, the driver sequence is added in excess to tester. (wikipedia.org)
  • However, despite the significant damage inflicted by M. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species. (pubmedcentralcanada.ca)
  • Although many mammalian host species may be compatible with MICROB Enrich , only human, mouse and rat rRNA sequences were used for the design and optimization of the capture oligonucleotides. (bio-medicine.org)
  • hybridization
  • Cyanine dyes are commonly used for fluorescent labeling of DNA and RNA oligonucleotides in applications including qPCR, sequencing, fluorescence in situ hybridization, Förster resonance energy transfer, and labeling for microarray hybridization. (jove.com)
  • Rapid amplification of cDNA ends (RACE) analysis using primers designed to these novel transcribed regions (called transcriptionally active regions [TARs] or TransFrags) followed by hybridization to arrays confirms the transcription of these regions. (biomedcentral.com)
  • Fluorescently labeled target sequences that bind to a probe sequence generate a signal that depends on the hybridization conditions (such as temperature), and washing after hybridization. (wikipedia.org)
  • They can then generate their own labeled samples for hybridization, hybridize the samples to the array, and finally scan the arrays with their own equipment. (wikipedia.org)
  • This technique was originally developed for the evaluation of the differences between the chromosomal complements of solid tumor and normal tissue, and has an improved resoIution of 5-10 megabases compared to the more traditional cytogenetic analysis techniques of giemsa banding and fluorescence in situ hybridization (FISH) which are limited by the resolution of the microscope utilized. (wikipedia.org)
  • The sequence signatures are deciphered by the parallel identification of four bases by hybridization to fluorescently labeled encoders (Figure 5). (wikipedia.org)
  • Each of the encoders has a unique label which is detected after hybridization by taking an image of the microbead array. (wikipedia.org)
  • The most important elements are, among others, hybridization ovens, chip scanners, and software packages for subsequent numerical analysis of the raw data. (wikipedia.org)
  • The hybridization signal intensities for each probe are used by specialized software to generate a log2ratio of test/normal for each probe on the array. (wikipedia.org)
  • tumors
  • From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangements in tumors. (bcgsc.ca)
  • The first report of CGH analysis was by Kallioniemi and colleagues in 1992 at the University of California, San Francisco, who utilised CGH in the analysis of solid tumors. (wikipedia.org)
  • transcript
  • However, this array analysis does not reveal information concerning transcript structure or abundance. (biomedcentral.com)
  • It also suffers from the same limitation of microarray analysis regarding the lack of correlation between transcript and protein levels. (wikipedia.org)
  • With respect to a gene, the two strands may be labeled the "template strand," which serves as a blueprint for the production of an RNA transcript, and the "coding strand," which includes the DNA version of the transcript sequence. (wikipedia.org)
  • bioinformatics
  • These experimental and bioinformatics analyses favor the hypothesis that exRNAs play a role in numerous biological processes. (wikipedia.org)
  • Bioinformatics is both an umbrella term for the body of biological studies that use computer programming as part of their methodology, as well as a reference to specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. (wikipedia.org)
  • Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data. (wikipedia.org)
  • commercially
  • However, in 1994 a review was published which described an easily understood protocol in detail and the image analysis software was made available commercially, which allowed CGH to be utilised all around the world. (wikipedia.org)
  • strains
  • We demonstrate here that marine cyanobacteria have a functionally active cyanase, the transcriptional regulation of which varies among strains and reflects the genomic context of cynS. (embl-heidelberg.de)
  • We present a comprehensive analysis of genome-wide measurements incorporating multifaceted holistic data - genome, transcriptome, proteome, and phenome - to determine the differences between Escherichia coli B and K-12 strains. (biomedcentral.com)
  • differences
  • Representational difference analysis (RDA) is a technique used in biological research to find sequence differences in two genomic or cDNA samples. (wikipedia.org)
  • The aim of this technique is to quickly and efficiently compare two genomic DNA samples arising from two sources, which are most often closely related, because it is suspected that they contain differences in terms of either gains or losses of either whole chromosomes or subchromosomal regions (a portion of a whole chromosome). (wikipedia.org)
  • It was concluded that the fluorescence ratios obtained were accurate and that differences between genomic DNA from different cell types were detectable, and therefore that CGH was a highly useful cytogenetic analysis tool. (wikipedia.org)
  • protein
  • This includes the analysis of the mutational DNA status and the RNA and protein expression levels of these specific genes to elucidate their role in the disease. (hindawi.com)
  • Structural analysis of the protein suggests that Annexin VII is a membrane binding protein with diverse properties including voltage-sensitive calcium channel activity, ion selectivity and membrane fusion. (wikipedia.org)
  • It also plays a role in the analysis of gene and protein expression and regulation. (wikipedia.org)
  • This includes nucleotide and amino acid sequences, protein domains, and protein structures. (wikipedia.org)
  • For example, there are methods to locate a gene within a sequence, to predict protein structure and/or function, and to cluster protein sequences into families of related sequences. (wikipedia.org)
  • Tiling arrays aid in transcriptome mapping as well as in discovering sites of DNA/protein interaction (ChIP-chip, DamID), of DNA methylation (MeDIP-chip) and of sensitivity to DNase (DNase Chip) and array CGH. (wikipedia.org)
  • In addition, proteases recruited from remote sources like nearby tissues are ignored by these DNA based arrays, reiterating the need for protein based methods to confirm the presence and activity of functional enzymes when transcriptome analysis is performed. (wikipedia.org)
  • tissue samples
  • Genomic characterization of 51 MPNST tissue samples identified several frequently amplified regions harboring 2,599 genes and regions of deletion including 4,901 genes. (aacrjournals.org)
  • parallel
  • Fluorescent imaging captures the signal from all of the beads, while affixed to a 2-dimensional surface, so DNA sequences are determined from all the beads in parallel. (wikipedia.org)
  • Firstly, drug discovery in the last decades leading up to the 1990s had been limited due to the time and cost of running many chromatographic analyses in parallel on macroscopic equipment. (wikipedia.org)
  • mammalian
  • In the first step of the MICROB Enrich procedure, host-bacterial total RNA is incubated with an optimized mixture of capture oligonucleotides that bind to the mammalian 18S and 28S rRNAs and polyadenylated RNAs. (bio-medicine.org)
  • available
  • In order to assure the best possible match for features across different microarray platforms, we used mappings that matched each feature to genomic information available from the NCBI Entrez gene database. (nih.gov)
  • Variants were further analyzed using clinical criteria and segregation analysis, where available. (ahajournals.org)
  • The motivation underlying the development of CGH stemmed from the fact that the available forms of cytogenetic analysis at the time (giemsa banding and FISH) were limited in their potential resolution by the microscopes necessary for interpretation of the results they provided. (wikipedia.org)
  • RNAtor RNAtor Android Application to calculate optimal parameters for popular tools and kits available for DNA sequencing projects. (wikipedia.org)