Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Sequencing Resource”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 361 records · Page 20Linked to original sources
PubMed2003

The musician's brain: functional imaging of amateurs and professionals during performance and imagery.

We compared activation maps of professional and amateur violinists during actual and imagined performance of Mozart's violin concerto in G major (KV216). Execution and imagination of (left hand) fingering movements of the first 16 bars of the concerto were performed. Electromyography (EMG) feedback was used during imagery training to avoid actual movement execution and EMG recording was employed during the scanning of both executed and imagined musical performances. We observed that professional musicians generated higher EMG amplitudes during movement execution and showed focused cerebral activations in the contralateral primary sensorimotor cortex, the bilateral superior parietal lobes, and the ipsilateral anterior cerebellar hemisphere. The finding that professionals exhibited higher activity of the right primary auditory cortex during execution may reflect an increased strength of audio-motor associative connectivity. It appears that during execution of musical sequences in professionals, a higher economy of motor areas frees resources for increased connectivity between the finger sequences and auditory as well as somatosensory loops, which may account for the superior musical performance. Professionals also demonstrated more focused activation patterns during imagined musical performance. However, the auditory-motor loop was not involved during imagined performances in either musician group. It seems that the motor and auditory systems are coactivated as a consequence of musical training but only if one system (motor or auditory) becomes activated by actual movement execution or live musical auditory stimuli.

Acoustic Stimulation↗
PubMed2003

The Proteome Analysis database: a tool for the in silico analysis of whole proteomes.

The Proteome Analysis database (http://www.ebi.ac.uk/proteome/) has been developed by the Sequence Database Group at EBI utilizing existing resources and providing comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archeae and eukaryotes. Three main projects are used, InterPro, CluSTr and GO Slim, to give an overview on families, domains, sites, and functions of the proteins from each of the complete genomes. Complete proteome analysis is available for a total of 89 proteome sets. A specifically designed application enables InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the database.

Animals↗
PubMed2005

XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis.

BACKGROUND: Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly important resource for researchers. To provide full advantage of the available sequence, we have analyzed 350,468 Xenopus laevis Expressed Sequence Tags (ESTs) both to identify full length protein encoding sequences and to develop a unique database system to support comparative approaches between X. laevis and other model systems. DESCRIPTION: Using a suffix array based clustering approach, we have identified 25,971 clusters and 40,877 singleton sequences. Generation of a consensus sequence for each cluster resulted in 31,353 tentative contig and 4,801 singleton sequences. Using both BLASTX and FASTY comparison to five model organisms and the NR protein database, more than 15,000 sequences are predicted to encode full length proteins and these have been matched to publicly available IMAGE clones when available. Each sequence has been compared to the KOG database and approximately 67% of the sequences have been assigned a putative functional category. Based on sequence homology to mouse and human, putative GO annotations have been determined. CONCLUSION: The results of the analysis have been stored in a publicly available database XenDB http://bibiserv.techfak.uni-bielefeld.de/xendb/. A unique capability of the database is the ability to batch upload cross species queries to identify potential Xenopus homologues and their associated full length clones. Examples are provided including mapping of microarray results and application of 'in silico' analysis. The ability to quickly translate the results of various species into 'Xenopus-centric' information should greatly enhance comparative embryological approaches.

Animals↗
PubMed2006

PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences.

We formerly released the porcine expressed sequence tag (EST) database Pig EST Data Explorer (PEDE; http://pede.dna.affrc.go.jp/), which comprised 68,076 high-quality ESTs obtained by using full-length-enriched cDNA libraries derived from seven tissues. We have added eight tissues and cell types to the EST analysis and have integrated 94,555 additional high-quality ESTs into the database. We also fully sequenced the inserts of 10,147 of the cDNA clones that had undergone EST analysis; the sequences and annotation of the cDNA clones were stored in the database. Further, we constructed an interface that can be used to perform various searches in the database. The PEDE database is the primary resource of expressed pig genes that are supported by full-length cDNA sequences. This resource not only enables us to pick cDNA clones of interest for a particular analysis, but it also confirms and thus contributes to the sequencing integrity of the pig genome, which is now being compiled by an international consortium (http://www.piggenome.org/). PEDE has therefore evolved into what we now call 'Pig Expression Data Explorer'.

Animals↗
PubMed2025

Single-cell glycome and transcriptome profiling enabled by a library of anti-glycan antibodies.

Glycans play critical roles in cellular processes and clinical applications, but they remain difficult to study due to a shortage of well-characterized anti-glycan reagents and high-throughput technologies for glycome profiling, especially ones capable of single-cell resolution. To meet these needs, we generated a database of 650 anti-glycan antibody sequences, recombinantly expressed a library of 154 antibodies, and extensively characterized their binding properties using glycan microarrays. In addition to providing valuable information and resources for the field, the sequence database and microarray data also enabled development of "Glycomic-seq" (Glycome profiling via multiplexed immunoglobulins combined with sequencing), a DNA-barcoded anti-glycan antibody platform that enables high-throughput, single-cell profiling of both RNA and cell-surface glycan expression. Using Glycomic-seq, we profiled two isogenic colorectal cancer cell lines. The results revealed various glycans associated with cancer stem cells and metastasis, demonstrating the power of integrating glycomic information with multi-omic efforts to discover biomarkers and therapeutic targets.

Polysaccharides↗
PubMed2003

Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp.

Expressed sequence tags (ESTs) are important resources for gene discovery and molecular marker development. From over 147,000 ESTs of Medicago truncatula, we have identified 4,384 ESTs containing perfect simple sequence repeats (EST-SSR) of di-, tri-, tetra- or pentanucleotides. Six hundred sixteen primer pairs (PPs) were designed and screened over a panel of eight genotypes representing six Medicago spp. and subspecies. Nearly, 74% (455) of the PPs produced characteristic SSR bands of expected size length in at least one Medicago species. Four hundred six (89%) of these 455 PPs produced SSR bands in all eight genotypes tested. Only 17 PPs were M. truncatula -specific. High levels of polymorphism (>70%) were detected for these markers in alfalfa, M. truncatula, and other annual medics. About 48% of the reported markers are part of gene transcripts linked to putative functions. Our results indicate that the SSR markers developed from M. truncatula ESTs are valuable genetic markers for the Medicago genus. These markers will be useful in establishing the genomic relationships of M. truncatula to important forage legume crops such as alfalfa and other annual medics.

Alleles↗
PubMed2006

CancerGenes: a gene selection resource for cancer genome projects.

The genome sequence framework provided by the human genome project allows us to precisely map human genetic variations in order to study their association with disease and their direct effects on gene function. Since the description of tumor suppressor genes and oncogenes several decades ago, both germ-line variations and somatic mutations have been established to be important in cancer-in terms of risk, oncogenesis, prognosis and response to therapy. The Cancer Genome Atlas initiative proposed by the NIH is poised to elucidate the contribution of somatic mutations to cancer development and progression through the re-sequencing of a substantial fraction of the total collection of human genes-in hundreds of individual tumors and spanning several tumor types. We have developed the CancerGenes resource to simplify the process of gene selection and prioritization in large collaborative projects. CancerGenes combines gene lists annotated by experts with information from key public databases. Each gene is annotated with gene name(s), functional description, organism, chromosome number, location, Entrez Gene ID, GO terms, InterPro descriptions, gene structure, protein length, transcript count, and experimentally determined transcript control regions, as well as links to Entrez Gene, COSMIC, and iHOP gene pages and the UCSC and Ensembl genome browsers. The user-friendly interface provides for searching, sorting and intersection of gene lists. Users may view tabulated results through a web browser or may dynamically download them as a spreadsheet table. CancerGenes is available at http://cbio.mskcc.org/cancergenes.

Databases, Genetic↗
PubMed2003

Gene identification through large-scale EST sequence processing.

The technology of sequencing expressed sequence tags (ESTs) offers a relatively cheap alternative to whole genome sequencing and has become a valuable resource for gene discovery. The inherent characteristics of ESTs, such as transcript redundancy, low sequence quality and high error rates, require processing of the sequences before any gene prediction can be made. The process includes EST pre-processing, analysis and similarity searches, and the data are generally stored in a database to organise the results and thereby assist the search for interesting genes.

Algorithms↗
PubMed1992

Pharmacoeconomic consequences of measurement and modification of hospital drug use.

Patterns of drug usage affect hospital-based delivery of healthcare in a variety of ways. Adverse reactions to drugs (ADR) precipitate some 5% of admissions and prejudice the care of some 20% of patients who are in hospital, while inadequate drug therapy prejudices outcomes and prolongs hospital stay. Conversely, appropriate application of drugs can promote recovery and increase the quality of care. Well documented examples include prevention of deep vein thrombosis and postoperative wound infections. Accordingly, optimisation of drug use represents a major quality assurance issue in addition to determining cost-efficiency of healthcare delivery. Drug utilisation review (DUR) requires all elements of the quality assurance process. In practice, therapeutically meaningful and cost-efficient exercises can only be mounted if there is knowledge of the linkage between patterns of drug use and clinical outcomes. These processes of measurement are currently rate-limiting in quality assurance. There are various ways that hospital drug usage can be measured. These range from readily available and relatively cheap quantitative methods to methods requiring the availability of expert staff. There is a sequence of methods involving increasing costs and increasing resource demands yielding increasing detail of information obtained. This sequence commences with pharmacy purchases, followed by pharmacy issues to particular clinical areas, prescription or treatment sheet survey, clinical record review, and finally the reports of trained investigators working in the clinical area. The simpler methods can provide useful information and an efficient basis for choosing and planning definitive studies. Once a category of drug use is appropriately targeted for intervention, drug use can be modified by planned intervention with improvement in clinical outcomes and reduced economic costs in many instances. The intervention strategies to modify drug usage may be classed as re-educative, persuasive, facilitative and power strategies. Other models for implementing behavioural change have been considered, including the impact of trained investigators and the use of online computer prescribing with interactive software with appropriate guidelines. The challenge is to achieve sustained change when interventions are implemented. Cost-efficient quality assurance of drug use is possible with modest resources if outcome-orientated activities are prioritised.

Drug Prescriptions↗
PubMed1988

Oligopeptide biases in protein sequences and their use in predicting protein coding regions in nucleotide sequences.

We have examined oligopeptides with lengths ranging from 2 to 11 residues in protein sequences that show no obvious evolutionary relationship. All sequences in the Protein Identification Resource database were carefully classified by sensitive homology searches into superfamilies to obtain unbiased oligopeptide counts. The results, contrary to previous studies, show clear prejudices in protein sequences. The oligopeptide preferences were used to help decide the significance of sequence homologies and to improve the more general methods for detecting protein coding regions within nucleotide sequences.

Amino Acid Sequence↗
PubMed2005

How can we use genomics to improve cereals with rice as a reference genome?

Rice serves as a model crop for cereal genomics. The availability of complete genome sequences, together with various genomic resources available for both rice and Arabidopsis, have revolutionized our understanding of the genetic make-up of crop plants. Both macrocolinearity revealed by comparative mapping and microcolinearity revealed by sequence comparisons among the grasses indicate that sequencing and functional analysis of the rice genome will have a significant impact on other cereals in terms of both genomic studies and crop improvement. The availability of mutants, introgression libraries, and advanced transformation techniques make functional genomics in rice and other cereals more manageable than ever before. A wide array of genetic markers, including anchor markers for comparative mapping, SSRs and SNPs are widely used in genetic mapping, germplasm evaluation and marker assisted selection. An integrated database that combines genome information for rice and other cereals is key to the effective utilization of all genomics resources for cereal improvement. To maximize the potential of genomics for plant breeding, experiments must be further miniaturized and costs must be reduced. Many techniques, including targeted gene disruption or allele substitution, insertional mutagenesis, RNA interference and homologous recombination, need to be refined before they can be widely used in functional genomic analysis and plant breeding.

Chromosome Mapping↗
PubMed1998

The PIR-International Protein Sequence Database.

From its origin the Protein Information Resource (http://www-nbrf. georgetown.edu/pir/) has supported research on evolution and computational biology by designing and compiling a comprehensive, quality controlled, and well-organized protein sequence database. The database has been produced and updated on a regular schedule since 1984. Since 1988 it has been maintained collaboratively by the PIR-International, an association of data collection centers engaged in international cooperation for the development of this research resource during a period of explosive acquisition of new data. As of June 1997, essentially all sequence entries have been classified into families, allowing the efficient application of methods to propagate and standardize annotation among related sequences. The databases are available through the Internet by the World-Wide Web and FTP, or on CD-ROM and magnetic media.

Amino Acid Sequence↗
PubMed1995

Chromosomal loci of 50 human keratinocyte cDNAs assigned by fluorescence in situ hybridization.

The chromosomal loci of expressed genes provide useful information for a candidate gene approach to the genes responsible for genetic diseases. A large set of randomly isolated cDNAs catalogued by partial sequencing can serve as a resource for accessing and isolating these disease genes. Using fluorescence in situ hybridization, we examined the chromosomal loci of 217 human keratinocyte-derived cDNAs, with independent novel sequence tags at the 3' end region. Among them, we determined the loci of 50 cDNAs. Single-pass sequencing of these from the 5' ends indicated that 39 cDNAs still can be produced for new genes. These cDNAs with identified chromosomal loci are powerful tools that can be used to help elucidate the genes responsible for hereditary skin disorders.

Chromosome Mapping↗
PubMed2005

Linkage mapping bovine EST-based SNP.

BACKGROUND: Existing linkage maps of the bovine genome primarily contain anonymous microsatellite markers. These maps have proved valuable for mapping quantitative trait loci (QTL) to broad regions of the genome, but more closely spaced markers are needed to fine-map QTL, and markers associated with genes and annotated sequence are needed to identify genes and sequence variation that may explain QTL. RESULTS: Bovine expressed sequence tag (EST) and bacterial artificial chromosome (BAC)sequence data were used to develop 918 single nucleotide polymorphism (SNP) markers to map genes on the bovine linkage map. DNA of sires from the MARC reference population was used to detect SNPs, and progeny and mates of heterozygous sires were genotyped. Chromosome assignments for 861 SNPs were determined by twopoint analysis, and positions for 735 SNPs were established by multipoint analyses. Linkage maps of bovine autosomes with these SNPs represent 4585 markers in 2475 positions spanning 3058 cM. Markers include 3612 microsatellites, 913 SNPs and 60 other markers. Mean separation between marker positions is 1.2 cM. New SNP markers appear in 511 positions, with mean separation of 4.7 cM. Multi-allelic markers, mostly microsatellites, had a mean (maximum) of 216 (366) informative meioses, and a mean 3-lod confidence interval of 3.6 cM Bi-allelic markers, including SNP and other marker types, had a mean (maximum) of 55 (191) informative meioses, and were placed within a mean 8.5 cM 3-lod confidence interval. Homologous human sequences were identified for 1159 markers, including 582 newly developed and mapped SNP. CONCLUSION: Addition of these EST- and BAC-based SNPs to the bovine linkage map not only increases marker density, but provides connections to gene-rich physical maps, including annotated human sequence. The map provides a resource for fine-mapping quantitative trait loci and identification of positional candidate genes, and can be integrated with other data to guide and refine assembly of bovine genome sequence. Even after the bovine genome is completely sequenced, the map will continue to be a useful tool to link observable phenotypes and animal genotypes to underlying genes and molecular mechanisms influencing economically important beef and dairy traits.

Alleles↗
PubMed2004

Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus).

Gene-derived markers are pivotal to the analysis of genome structure, organization, and evolution and necessary for comparative genomics. However, gene-derived markers are relatively difficult to develop. This project utilized the genomic resources of channel catfish expressed sequence tags (ESTs) to identify simple sequence repeats (SSRs), or microsatellites. It took the advantage of ESTs for the establishment of gene identities, and of microsatellites for the acquisition of high polymorphism. When microsatellites are tagged to genes, the microsatellites can then be used as gene markers. A bioinformatic analysis of 43,033 ESTs identified 4855 ESTs containing microsatellites. Cluster analysis indicated that 1312 of these ESTs fell into 569 contigs, and the remaining 3534 ESTs were singletons. A total of 4103 unique microsatellite-containing genes were identified. The dinucleotide CA/TG and GA/TC pairs were the most abundant microsatellites. AT-rich microsatellite types were predominant among trinucleotide and tetranucleotide microsatellites, consistent with our earlier estimation that the catfish genome is highly AT-rich. Our preliminary results indicated that the majority of the identified microsatellites were polymorphic and, therefore, useful for genetic linkage mapping of catfish. Mapping of these gene-derived markers is under way, which will set the foundation for comparative genome analysis in catfish.

Animals↗
PubMed1980

Genetic variability of alcohol dehydrogenase among Australian Drosophila species: correlation of ADH biochemical phenotype with ethanol resource utilization.

Alcohol dehydrogenase (ADH) activities, electrophoretic phenotypes, and the extent of ethanol resource utilization are compared for three groups of species distinguishable on ecological criteria: 1) the cosmopolitan species D. melanogaster, a frequent inhabitant of wineries; 2) fruit-baited species of the typically Australian subgenus Scaptodrosophila: D. lativittata, D. nitidithorax and D. howensis; and 3) Scaptodrosophila species not attracted to fermented-fruit baits being collected by sweeping in temperate rain forests (D. inornata, D. collessi) or from Hibiscus flowers (D. hibisci). D. melanogaster showed the highest levels of ADH activity and an electrophoretic polymorphism with two active allelic forms, while group 2) species showed intermediate ADH activities and polymorphisms, which were consistent with "high activity" and "low activity" allelic forms in natural populations of these species, and group 3) species showed only "low activity" forms. Ethanol resource utilization follows the same sequence, being 1 greater than 2 greater than 3 (D. howensis and D. collessi were not tested). Therefore the species considered show an association of ADH biochemical phenotype, laboratory ethanol utilization, and resources utilized.

Alcohol Oxidoreductases↗
PubMed2004

Parasite genome databases and web-based resources.

In the last decade, high-throughput genome sequencing and complementary techniques such as microarray and proteomics have generated, and will continue to generate, ever-increasing amounts of data. These technologies of gene discovery, expression, and functional analysis have been applied to a vast array of organisms, including parasites. In most instances, the data are freely available via the Internet, and researchers are becoming increasingly reliant on up-to-date, centralized data repositories to complement wet bench science. This chapter presents an overview of resources relevant to researchers with an interest in para-site genomics and biology. After briefly touching on some of the publicly available nucleotide and protein sequence as well as domain databases, the focus turns to parasite genome projects and associated Web-based resources. A list of parasite sequencing projects current at the time of writing, including relevant Web site addresses, is provided. The available resources range from network sites and project pages at sequencing institutes to databases that integrate and curate sequence data and associated annotation with diverse biological datasets. Particular attention is given to three databases, GeneDB (http://www.genedb.org/), PlasmoDB (http://plasmodb. org/), and tigr db, detailing the scope of each database and the tools available for data querying and retrieval.

Animals↗
PubMed1980

Music as a vehicle for life enrichment and expanded content for special audiences.

Music for special audiences has been a neglected part of most programs. The primary problem has been lack of understanding of the advantages of music and where it fits into a curriculum. Another problem has been the lack of skill to execute an effective program. Most musical events have been isolated with little continuity from one activity to another. Another programming difficulty has been where to find resources and how to use them. The purpose of this article is to briefly discuss programming for special audiences. An illustrative exercise has been provided to point out a programming format, especially the sequencing among activities and the resource utilization dimensions.

Adolescent↗