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 721 records · Page 40Linked to original sources
PubMed2005

Analysis of testis-specific transcripts in the chicken.

Sequences of candidate chicken testis-specific genes were analysed in order to develop a resource for functional genomic studies of the testis and male germ cells. Tentative consensus sequences (TC) containing expressed sequence tags expressed in testis libraries were selected from the TIGR Gallus gallus Gene Index, resulting in 292 TC. The transcriptional expression of these genes were evaluated in several chicken tissues, including testis and ovary. One hundred ten of the 292 TC were expressed in a testis-specific manner. Annotation of the TC using the Gene Ontology database terms showed that the proportion of testis-specific TC that were classified as having catalytic activity (within the molecular function branch) was higher than the proportion of total chicken TC classified in the same way. Our results may facilitate the investigation of testis-specific genes and their functional analysis in the chicken, as well as in other avian species.

Animals↗
PubMed1998

Biochemical characterization of bovine alpha s1-casein F and genotyping with sequence-specific primers.

Bovine alpha s1-casein F (alpha s1-CN F) was found in a genetic resource of Deutsches Schwarzbuntes Niederungsrind cows at a frequency of 0.009. Biochemical characterization of this new variant was obtained by automated sequencing of reversed-phase HPLC-separated tryptic peptides of alpha s1-CN F and alpha s1-CN B. alpha s1-CN F was found to be a subtype of alpha s1-CN B with a single amino acid substitution (SerP/Leu) in position 66. DNA sequencing revealed a C/T transition in position 8418 of the gene. Sequence-specific primers were designed to perform an allele-specific polymerase chain reaction for detection of alpha s1 CnF. Typing of artificial insemination sperm samples included in the genetic resource sperm pool identified one sire heterozygous for alpha s1 CnF.

Alleles↗
PubMed2005

Evaluation of an oligonucleotide ligation assay for detection of mutations in HIV-1 subtype C individuals who have high level resistance to nucleoside reverse transcriptase inhibitors and non-nucleoside reverse transcriptase inhibitors.

The oligonucleotide ligation assay (OLA) has been proposed as an affordable alternative to sequence-based HIV-1 drug resistance testing in resource poor settings. The aim was to evaluate OLA for detecting mutations K103N, Y181C, K65R, Q151M, M184V and T215Y/F in subtype C. Forty-four subtype C and 8 subtype B HIV-1 positive individuals were analysed using the ViroSeqtrade mark HIV-1 genotyping assay (Applied Biosystems, Foster City, CA). A one-step RT-PCR and nested PCR were performed using subtype B specific primers from the OLA kit (NIH AIDS Research and Reference Reagent Program). Seventy-eight subtype C sequences were used to design subtype C specific primers. Ligation and detection steps were followed according to OLA kit protocol. For codons, K103N, Y181C, K65R, Q151M, M184V and T215Y/F, four or more mismatches compared to the probe or mismatches less than four bases from the ligation site were not tolerated. Results revealed accurate identification of mutations in 2/10, 4/9 3/9, 6/7, 2/7 and 6/7 VQA samples and 5/20, 4/17 0/20, 18/24, 5/24 and 13/24 subtype C positive individuals, respectively. It was concluded that the probes and primers in the NIH reference kit would need modification to optimize detection of mutations in subtype C individuals.

Anti-HIV Agents↗
PubMed2006

Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat.

BACKGROUND: Our understanding of the mechanisms that govern the cellular process of meiosis is limited in higher plants with polyploid genomes. Bread wheat is an allohexaploid that behaves as a diploid during meiosis. Chromosome pairing is restricted to homologous chromosomes despite the presence of homoeologues in the nucleus. The importance of wheat as a crop and the extensive use of wild wheat relatives in breeding programs has prompted many years of cytogenetic and genetic research to develop an understanding of the control of chromosome pairing and recombination. The rapid advance of biochemical and molecular information on meiosis in model organisms such as yeast provides new opportunities to investigate the molecular basis of chromosome pairing control in wheat. However, building the link between the model and wheat requires points of data contact. RESULTS: We report here a large-scale transcriptomics study using the Affymetrix wheat GeneChip(R) aimed at providing this link between wheat and model systems and at identifying early meiotic genes. Analysis of the microarray data identified 1,350 transcripts temporally-regulated during the early stages of meiosis. Expression profiles with annotated transcript functions including chromatin condensation, synaptonemal complex formation, recombination and fertility were identified. From the 1,350 transcripts, 30 displayed at least an eight-fold expression change between and including pre-meiosis and telophase II, with more than 50% of these having no similarities to known sequences in NCBI and TIGR databases. CONCLUSION: This resource is now available to support research into the molecular basis of pairing and recombination control in the complex polyploid, wheat.

Chromosome Pairing↗
PubMed2005

PatMatch: a program for finding patterns in peptide and nucleotide sequences.

Here, we present PatMatch, an efficient, web-based pattern-matching program that enables searches for short nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small domains and motifs in protein sequences. The program can be used to find matches to a user-specified sequence pattern that can be described using ambiguous sequence codes and a powerful and flexible pattern syntax based on regular expressions. A recent upgrade has improved performance and now supports both mismatches and wildcards in a single pattern. This enhancement has been achieved by replacing the previous searching algorithm, scan_for_matches [D'Souza et al. (1997), Trends in Genetics, 13, 497-498], with nondeterministic-reverse grep (NR-grep), a general pattern matching tool that allows for approximate string matching [Navarro (2001), Software Practice and Experience, 31, 1265-1312]. We have tailored NR-grep to be used for DNA and protein searches with PatMatch. The stand-alone version of the software can be adapted for use with any sequence dataset and is available for download at The Arabidopsis Information Resource (TAIR) at ftp://ftp.arabidopsis.org/home/tair/Software/Patmatch/. The PatMatch server is available on the web at http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl for searching Arabidopsis thaliana sequences.

Arabidopsis↗
PubMed2002

Genomic BLAST: custom-defined virtual databases for complete and unfinished genomes.

BLAST (Basic Local Alignment Search Tool) searches against DNA and protein sequence databases have become an indispensable tool for biomedical research. The proliferation of the genome sequencing projects is steadily increasing the fraction of genome-derived sequences in the public databases and their importance as a public resource. We report here the availability of Genomic BLAST, a novel graphical tool for simplifying BLAST searches against complete and unfinished genome sequences. This tool allows the user to compare the query sequence against a virtual database of DNA and/or protein sequences from a selected group of organisms with finished or unfinished genomes. The organisms for such a database can be selected using either a graphic taxonomy-based tree or an alphabetical list of organism-specific sequences. The first option is designed to help explore the evolutionary relationships among organisms within a certain taxonomy group when performing BLAST searches. The use of an alphabetical list allows the user to perform a more elaborate set of selections, assembling any given number of organism-specific databases from unfinished or complete genomes. This tool, available at the NCBI web site http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi, currently provides access to over 170 bacterial and archaeal genomes and over 40 eukaryotic genomes.

Amino Acid Sequence↗
PubMed1995

Visuospatial working memory, movement control and executive demands.

Developments in the concept of a specialist visuospatial resource in working memory owe much to a pair of tasks originally developed by Brooks (1967), involving respectively the generation and retention of a mental image of a matrix pattern and the retention of a verbal sequence. Previous literature has demonstrated that the matrix task calls on cognitive resources which are involved in both the processing of visual input and the generation of movement sequences. Using dual task methodology, the study reported here demonstrates that the matrix and verbal versions of the task do indeed rely on separate, specialized cognitive resources, one of which is also involved in generation of action. However, when the secondary task (random generation of numbers) was very demanding of general purpose cognitive resources both the matrix and verbal tasks were performed poorly, suggesting that each of these tasks draw heavily on a common, general purpose resource as well as on their respective specialist resources. It is argued that random generation offers a means to assess general purpose cognitive resources and that the cognitive processes involved in the Brooks tasks may be more complex than has been previously assumed.

Adult↗
PubMed1990

Split-mouth and cross-over designs in dental research.

The presence of paired or multiple organs (arches, quadrants, teeth) and the chronic nature of many dental diseases suggest the use of split-mouth (trials in which each subject receives greater than or equal to 2 treatments, each to a separate section of the mouth) and cross-over research designs (trials in which each subject receives greater than or equal to 2 treatments in sequence). While these designs offer potential savings in resources, their usefulness can be negated if several strict scientific and statistical assumptions are not met. The primary prerequisites for the use of split-mouth and cross-over designs are that: (1) the disease to be investigated is relatively stable and uniformly distributed; (2) the effects of the treatments to be evaluated are short-lived or reversible for cross-over studies, or are localized for split-mouth designs. Other important factors that influence the appropriate use of these designs include: the method of treatment sequencing and assignment, and the cross-over rules used; blinding of patient assignment, patients and observers; assessment of order effects including period, carry-over or spill-over effects; the choice of statistical analysis, the sample size utilized, and the special importance of patients lost to study or of faulty data points. The objective of this study was to review 3 journals for studies using split-mouth or cross-over designs to determine how the assumptions underlying these research designs are considered and applied in dental research. The majority of studies used adequate methods for treatment allocation and sequencing; however, many studies failed to take advantage of the research designs in the statistical analysis of data. In addition, very few studies considered the possibility of order effects or reduced bias through blinding procedures.

Clinical Trials as Topic↗
PubMed1989

Computers: the best friends a human genome ever had.

Mapping and sequencing the human genome will generate large amounts of data, which must be sorted, analyzed, and stored for rapid retrieval to complete this enormous task. Computers and their software programs provide the most important tool to the molecular biologist today. A discussion of current capabilities and future needs in computer hardware and software for the human genome project is the topic of this paper. The use of computer programs to generate restriction maps, manage clone libraries, manage sequence projects, and generate consensus sequences is presented. The use of computers to communicate useful information rapidly to scientific colleagues is also mentioned. The role of both GenBank and BIONET is central to the dissemination and analysis of sequence information. The capabilities of electronic communication worldwide for assisting this project is available on the BIONET National Computer Resource, using existing networks.

Base Sequence↗
PubMed1994

Molecular genetics of the most endangered canid: the Ethiopian wolf Canis simensis.

The world's most endangered canid is the Ethiopian wolf Canis simensis, which is found in six isolated areas of the Ethiopian highlands with a total population of no more than 500 individuals. Ethiopian wolf populations are declining due to habitat loss and extermination by humans. Moreover, in at least one population, Ethiopian wolves are sympatric with domestic dogs, which may hybridize with them, compete for food, and act as disease vectors. Using molecular techniques, we address four questions concerning Ethiopian wolves that have conservation implications. First, we determine the relationships of Ethiopian wolves to other wolf-like canids by phylogenetic analysis of 2001 base pairs of mitochondrial DNA (mtDNA) sequence. Our results suggest that the Ethiopian wolf is a distinct species more closely related to gray wolves and coyotes than to any African canid. The mtDNA sequence similarity with gray wolves implies that the Ethiopian wolf may hybridize with domestic dogs, a recent derivative of the gray wolf. We examine this possibility through mtDNA restriction fragment analysis and analysis of nine microsatellite loci in populations of Ethiopian wolves. The results imply that hybridization has occurred between female Ethiopian wolves and male domestic dogs in one population. Finally, we assess levels of variability within and between two Ethiopian wolf populations. Although these closely situated populations are not differentiated, the level of variability in both is low, suggesting long-term effective population sizes of less than a few hundred individuals. We recommend immediate captive breeding of Ethiopian wolves to protect their gene pool from dilution and further loss of genetic variability.

Animals↗
PubMed2004

Infiltration by alien predators into invertebrate food webs in Hawaii: a molecular approach.

Abstract Alien invertebrate predators have been introduced to Hawaii to control pests, particularly in lowland areas where most crops are grown. We developed techniques for assessing the impact of these predators on native food webs in relatively pristine upland areas where, it was hypothesized, few lowland predators might be found. Predator densities were assessed along transects within the Alakaii Swamp on Kaua'i. The most numerous alien biocontrol agents found were Halmus chalybeus (Coccinellidae), a species known to feed on Lepidoptera eggs. Laboratory experiments were conducted using two genera of endemic Lepidoptera, Scotorythra and Eupithecia (Geometridae), that are of considerable conservation value, the former because of its recent speciation across Hawaii, the latter for its unique predatory larvae. Techniques were developed for detecting Lepidoptera DNA within the guts of alien predators using prey-specific PCR primers. General primers amplified fragments of the mitochondrial cytochrome oxidase I gene from beetles and Lepidoptera. The sequences were aligned and used successfully to design target-specific primers for general detection of the remains of Geometridae and for particular species, including Scotorythra rara and Eupithecia monticolans. DNA fragments amplified were short [140-170 base pairs (bp)], optimizing detection periods following prey ingestion. Trials using the introduced biocontrol agent Curinus coeruleus (Coccinellidae) demonstrated detection of Lepidoptera DNA fragments = 151 bp in 85-100% of beetles after 24 h digestion of an early instar larva. This study provides a framework for future use of molecular gut analysis in arthropod conservation ecology and food web research with considerable potential for quantifying threats to endemic species in Hawaii and elsewhere.

Amino Acid Sequence↗
PubMed2004

The effect of the last glacial age on speciation and population genetic structure of the endangered Ethiopian wolf (Canis simensis).

During the last glacial age, Afro-alpine habitats were widespread across the highlands of Ethiopia. A wolf-like canid ancestor is thought to have colonized this expanding habitat and given rise to a new species that was remarkably well adapted to the high altitude environment: the Ethiopian wolf Canis simensis. Here, we address the timing of genetic divergence and examine population genetic history and structure by investigating the distribution of mitochondrial DNA (mtDNA) sequence variation. The pattern of mtDNA variation and geographical distribution indicate an initial population expansion, probably immediately after divergence from the wolf-like ancestor, around 100,000 years ago. The partition of mtDNA haplotypes that followed was most likely the result of habitat reduction and fragmentation at the onset of deglaciation approximately 15,000 years ago. Phylogenetic and geographical associations suggest that the most likely genetic partitioning corresponds to three mountain areas, Arsi/Bale, Wollo/Shoa and Simien/Mt. Guna. Although there is a degree of clustering of haplotypes from both sides of the Rift Valley, the lack of reciprocal monophyly does not support the taxonomic classification of two subspecies. This study highlights the importance of populations north of the Rift Valley for the maintenance of genetic variability within the species and has consequent implications for conservation.

Analysis of Variance↗
PubMed2004

Species boundaries, phylogeography and conservation genetics of the red-legged frog (Rana aurora/draytonii) complex.

The red-legged frog, Rana aurora, has been recognized as both a single, polytypic species and as two distinct species since its original description 150 years ago. It is currently recognized as one species with two geographically contiguous subspecies, aurora and draytonii; the latter is protected under the US Endangered Species Act. We present the results of a survey of 50 populations of red-legged frogs from across their range plus four outgroup species for variation in a phylogenetically informative, approximately 400 base pairs (bp) fragment of the mitochondrial cytochrome b gene. Our mtDNA analysis points to several major results. (1) In accord with several other lines of independent evidence, aurora and draytonii are each diagnosably distinct, evolutionary lineages; the mtDNA data indicate that they do not constitute a monophyletic group, but rather that aurora and R. cascadae from the Pacific northwest are sister taxa; (2) the range of the draytonii mtDNA clade extends about 100 km further north in coastal California than was previously suspected, and corresponds closely with the range limits or phylogeographical breaks of several codistributed taxa; (3) a narrow zone of overlap exists in southern Mendocino County between aurora and draytonii haplotypes, rather than a broad intergradation zone; and (4) the critically endangered population of draytonii in Riverside County, CA forms a distinct clade with frogs from Baja California, Mexico. The currently available evidence favours recognition of aurora and draytonii as separate species with a narrow zone of overlap in northern California.

Animals↗
PubMed2006

Comparison of methods for genomic localization of gene trap sequences.

BACKGROUND: Gene knockouts in a model organism such as mouse provide a valuable resource for the study of basic biology and human disease. Determining which gene has been inactivated by an untargeted gene trapping event poses a challenging annotation problem because gene trap sequence tags, which represent sequence near the vector insertion site of a trapped gene, are typically short and often contain unresolved residues. To understand better the localization of these sequences on the mouse genome, we compared stand-alone versions of the alignment programs BLAT, SSAHA, and MegaBLAST. A set of 3,369 sequence tags was aligned to build 34 of the mouse genome using default parameters for each algorithm. Known genome coordinates for the cognate set of full-length genes (1,659 sequences) were used to evaluate localization results. RESULTS: In general, all three programs performed well in terms of localizing sequences to a general region of the genome, with only relatively subtle errors identified for a small proportion of the sequence tags. However, large differences in performance were noted with regard to correctly identifying exon boundaries. BLAT correctly identified the vast majority of exon boundaries, while SSAHA and MegaBLAST missed the majority of exon boundaries. SSAHA consistently reported the fewest false positives and is the fastest algorithm. MegaBLAST was comparable to BLAT in speed, but was the most susceptible to localizing sequence tags incorrectly to pseudogenes. CONCLUSION: The differences in performance for sequence tags and full-length reference sequences were surprisingly small. Characteristic variations in localization results for each program were noted that affect the localization of sequence at exon boundaries, in particular.

Algorithms↗
PubMed2005

The Ixodes scapularis Genome Project: an opportunity for advancing tick research.

The Ixodes scapularis Genome Project (IGP), the first to sequence a tick genome, will provide an unparalleled resource for studying tick biology and tick-host-pathogen relationships, and identifying novel targets for tick and tick-borne disease control. The IGP will be the first genomic analysis of a member of the subphylum Chelicerata and will accelerate the pace of tick research. The challenge for scientists is to translate IGP data into public health benefits.

Animals↗
PubMed2001

[A comparison of the its sequences of the Tibetan medicine "zang yin chen"--Swertia mussotti and its adulterant species].

AIM: To identify the medicine and search for new medicine resource at the molecular level, the ITS of "Zang Yin Chen"--Swertia mussotti and its adulterant species were sequenced. METHODS: The double-stranded DNA was amplified using PCR systems 9,600 kits and sequenced on an ABI 377 automated sequencer from both directions. RESULTS: The ITS sequences of S. mussotti in different populations showed no variation. It has the unique ITS sequence and shows distinct difference from its adulterant species. In the phylogenetic tree based on the ITS data of S. mussotti and all vicarious species constructed by Paup, S. franchetiana and S. mussotti clustered together with high bootstrap support. CONCLUSION: ITS sequences can be used for the molecular authentication between the S. mussotti and its adulterant species. S. franchetiana can be regarded as a new medicine resource of "Zhang Yin Chen".

Base Sequence↗
PubMed1999

GIST: A web tool for collecting gene information.

As the human genome is sequenced and annotated, an important step in future genetic studies of complex traits and diseases will be the identification of relevant candidate genes. To enable such compilations, it would be useful to collate all necessary and available genetic information for each candidate gene. To this end, we have created a web tool (http://genome.cwru.edu/gist/gist.html+ ++) to allow the rapid cataloging of currently available genetic data. This tool, called GIST (or "Gene Information Search Tool"), allows an investigator to search the major genomic databases containing gene and marker information from a single query point. To prove the utility of GIST, a catalog of 150 hypertension candidate genes was created. This resource collates all available nucleotide and amino acid sequence data, expression data, chromosomal map location, and genetic marker interval for each gene, collected from on-line databases. These data can be used to guide genetic studies of hypertension.

Databases, Factual↗