• Here, we describe the isolation and characterization of expressed sequence tags (ESTs) isolated from a chicken pineal gland cDNA library. (westminster.ac.uk)
  • 6% of the ESTs matched neither GenBank cDNA sequences nor the newly assembled chicken genomic DNA sequence, three ESTs aligned with sequences designated to be on the Z_random, while one matched a W chromosome sequence and could be useful in cataloguing functionally important genes on this sex chromosome. (westminster.ac.uk)
  • Additionally, single nucleotide polymorphisms (SNPs) were identified and validated in 10 ESTs that showed 98% or higher sequence similarity to known chicken genes. (westminster.ac.uk)
  • Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). (nih.gov)
  • From the two cDNA-libraries 24,000 ESTs were collected and a total of 2200 unigenes have been sequenced and annotated ( www.marinegenomics.org ). (vin.com)
  • The objectives of this study were to construct a normalized cDNA library for efficient EST analysis, to generate thousands of ESTs, and to analyze the ESTs for microsatellites and potential single nucleotide polymorphisms (SNPs). (nih.gov)
  • A total of 35 microsatellites were identified from the ESTs, with 18 having sufficient flanking sequences for primer design. (nih.gov)
  • A total of 5,542 ESTs were generated representing 4,688 unique sequences. (nih.gov)
  • cDNAs averaged 500-600 bp in length and were treated as expressed sequence tags (ESTs). (mpg.de)
  • Clustering analysis of 805 random cDNAs resulted in 179 and 155 different ESTs for the oxic and anoxic zones respectively. (mpg.de)
  • A total of 600,000 sequencing attempts were made, generating a total of 438,321 quality ESTs. (auburn.edu)
  • In order to select reliable SNPs, contigs containing four or more ESTs should be used and the minor allele sequence should be represented at least twice. (auburn.edu)
  • Application of such quality assessment measures, along with large resources of ESTs, should provide effective means for SNP identification in species where genome sequence resources are lacking. (auburn.edu)
  • Single pass sequencing of such libraries will be used to create a catalogue of Expressed Sequence Tags (ESTs) that will be used to develop single nucleotide polymorphic (SNP) markers. (europa.eu)
  • The leaves were harvested at various times after cold stress for total RNA extraction, which was used to generate expressed sequence tags (ESTs). (geneticsmr.com)
  • After randomly choosing, cloning and sequencing, 227 ESTs with high quality were obtained and submitted to GenBank database. (geneticsmr.com)
  • Using BLASTX, 79.7% of the ESTs shared homology with known functional DNA sequences and 20.3% shared significant homology with unknown proteins. (geneticsmr.com)
  • National Centre for Biotechnology Information (NCBI): cDNA libraries and Expressed Sequence Tags (ESTs), EST analysis, Pairwise alignment techniques, Multiple sequence alignment. (cutm.ac.in)
  • Results We describe a bioinformatics pipeline known as FunnyBase that has been used to store, annotate, and analyze 40,363 expressed sequence tags (ESTs) from the heart and liver of the fish, Fundulus heteroclitus. (umsystem.edu)
  • Expressed sequenced tags (ESTs) of 1 019 randomly selected clones were analyzed and then assembled 588 unigens. (korea.ac.kr)
  • Among the matched sequences, ESTs were identified from tissues other than berries or from berries at different developmental stages. (biomedcentral.com)
  • Additional MPSS signatures not matching to known grape ESTs can extend our knowledge of the V. vinifera transcriptome, particularly when these data are used to assist in annotation of whole genome sequences from Vitis vinifera . (biomedcentral.com)
  • The Atlantic Cod Genomics and Broodstock Development Project (www.codgene.ca) aims to generate an extensive set of molecular tools for cod, including a database containing approximately 160,000 expressed sequence tags (ESTs). (canada.ca)
  • To date approximately 25,000 ESTs have been generated from normalized cDNA libraries representing various tissues (e.g. gonad, liver, heart, gill, brain), and suppression subtractive hybridization (SSH) libraries are being created for the purpose of identifying cod genes responsive to immunogens or environmental stress. (canada.ca)
  • In this study, a suppression subtractive hybridization cDNA library approach was used for the identification of pathogen and plant genes that were differentially expressed during infection of the susceptible cultivar BRS Pérola of Phaseolus vulgaris L. A total of 979 unigenes (430 contigs and 549 singletons) were obtained and classified according to their functional categories. (frontiersin.org)
  • These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. (nih.gov)
  • The 2200 unigenes from the EST collection and the 62 immune-function targeted genes, together with other genes randomly selected without sequencing from the cDNA libraries, have been amplified and used to construct a cDNA microarray representing 3700 dolphin genes in duplicate for a total of 7400. (vin.com)
  • The cDNA dolphin array will be used to analyze PBL RNA from captive and wild dolphins of known health status with the aim to validate and optimize the cDNA microarray as a sensitive and informative tool for dolphin health assessment. (vin.com)
  • Gene expression was measured by hybridization of fluorescently labeled cDNA (preovulatory estrogenic or -luteinized) to the microarray. (appliedbioinfo.com)
  • A total of 389 unigenes had significant homologies with known protein sequences at the NCBI database and the remaining 199 unigenes were designated unidentified genes. (korea.ac.kr)
  • Bioinformatic analysis showed that AhLPAT was composed of eleven exons and ten introns with typical GT-AG characteristic in comparison of its sequences of genomic DNA and cDNA by Splign in NCBI. (chinacrops.org)
  • In silico comparison of cDNA libraries identified aphid genes with tissue-specific expression patterns, and gene expression that is induced by feeding on Nicotiana benthamiana. (nih.gov)
  • Entrez is NCBI's primary text search and retrieval system that integrates the PubMed database of biomedical literature with 38 other literature and molecular databases including DNA and protein sequence, structure, gene, genome, genetic variation and gene expression. (nih.gov)
  • Nuclear genome sequence and gene expression of an intracellular fungal endophyte stimulating the growth of cranberry plants. (umontreal.ca)
  • Two cDNA libraries from known health status dolphin PBL have been generated including an IL-2 and an LPS-stimulated cDNA library, respectively biased towards T and B-cell gene expression. (vin.com)
  • Quantitative PCR and high-throughput methods, such as expressed sequence tag analysis, have been used for measuring gene expression and identifying subsets of elm genes that are differentially expressed in the presence of O. novo-ulmi . (sisef.it)
  • Expressed Sequence Tag (EST) sequencing is one of the most efficient means for gene discovery and gene expression profiling. (auburn.edu)
  • BACKGROUND: Long terminal repeat (LTR)-retrotransposons (LTR-RTs) are ubiquitous and make up the majority of nearly all sequenced plant genomes, whereas their pivotal roles in genome evolution, gene expression regulation as well as their epigenetic regulation are still not well understood, especially in a large number of closely related species. (bvsalud.org)
  • Almost 2,000 expressed sequence tag (EST) cDNA clones were sequenced to analyze gene expression in control and Cd-treated leaf trichomes. (uni-bayreuth.de)
  • Gene expression was studied by cDNA microarrray analyses using 4608 unique clones from liver-derived expressed sequence tag (EST) libraries fortified with clones of known liver genes representing ∼4000 genes. (houstonmethodist.org)
  • 2014). Where annotations were not present or were different, the online Softberry server (http://linux1.softberry.com/berry.phtml) was used to predict mRNA and protein sequences using the FGNESH+ prediction algorithm (Solovyev et al. (molquest.com)
  • The BioProject database is a searcheable collection of complete and incomplete (in-progress) large-scale molecular projects including genome sequencing and assembly, transcriptome, metagenomic, annotation, expression and mapping projects. (nih.gov)
  • Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally utilized in downstream analyses. (umsystem.edu)
  • We constructed a full-length cDNA library of peanut ( Arachis hypogaea ) seed via a large number of sequences of expressed sequence tag (EST) and gene functional annotation, a lysophosphatidic acid acyltransferase gene, designated AhLPAT, and its genomic DNA sequence were isolated from peanut. (chinacrops.org)
  • However, the lack of a reference genome sequence hampers research progress for both academic and applied purposes. (biomedcentral.com)
  • The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. (biomedcentral.com)
  • Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome. (biomedcentral.com)
  • Until recently, however, functional analysis of the DED fungi was hampered by the lack of protocols for efficient gene knockout and by the unavailability of a full genome sequence. (sisef.it)
  • Random Expressed Sequence Tag (EST) clones have been isolated and sequenced from dolphin Peripheral Blood Leukocyte (PBL) cDNA libraries. (vin.com)
  • Bacterial artificial chromosome clones have been isolated from a trout library to further facilitate genomic characterization. (usda.gov)
  • These analyses have also helped identify genes that were differentially expressed in DED fungi grown under defined experimental conditions. (sisef.it)
  • Of these, 17 were identical or homologous to known mammalian cDNAs or expressed sequence tags. (diabetesjournals.org)
  • Three introns were identified in the rainbow trout, Atlantic salmon and zebrafish genomic sequences, and the intron locations correspond closely to those in the mammalian TNFSF 13b genes. (usda.gov)
  • Here, we have described resources that may be useful in comparative and functional genomic analysis of genes expressed in an important organ, the pineal gland, in a model and agriculturally important organism. (westminster.ac.uk)
  • In: Expressed sequence tags - generation and analysis, Methods in Molecular Biology Vol. 533 (J. Parkinson, ed. (umontreal.ca)
  • Cluster analysis indicated the presence of 635 contigs and 4,053 singletons, generating a total of 4,688 unique sequences. (nih.gov)
  • In summary, the soil metatranscriptome is accessible for global analysis and such studies have great potential in elucidating the taxonomic and functional status of soil bacterial communities, but study significance depends on the number and length of cDNAs being randomly analysed. (mpg.de)
  • An analysis of 555 randomly chosen clones in the library showed that 80 were derived from abundant mRNAs and were accounted for by 29 distinct sequences. (diabetesjournals.org)
  • In 1993 Søren Brunak became the founding Director of the Center for Biological Sequence Analysis (CBS) at the Technical University of Denmark (DTU), heading a multi-disciplinary research group of molecular biologists, biochemists, medical doctors, physicists, and computer scientists. (ku.dk)
  • In this study, we thoroughly examined the repetitive components of male and female H. scandens using next-generation sequencing data followed by bioinformatics analysis and florescence in situ hybridization (FISH). (bvsalud.org)
  • This study improves our understanding of the repetitive sequence organization of H. scandens genome and provides a basis for further analysis of their chromosome evolution process. (bvsalud.org)
  • Reverse transcription-PCR (RT-PCR) analysis demonstrated that antipathogenic T-phylloplanin-like proteins, glutathione peroxidase and several classes of pathogenesis-related (PR) proteins were expressed specifically or dominantly in trichomes. (uni-bayreuth.de)
  • An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. (umsystem.edu)
  • Therefore, we constructed a cDNA library using algal cells grown at exponential growth phase and carried out expressed sequence tag (EST) analysis. (academicconcepts.net)
  • Analysis of an F2 mapping population indicated the genes are tightly linked in HN1, and bacterial artificial chromosome sequencing confirmed they exist as a complex gene cluster for plant alkaloids. (ampliconexpress.com)
  • Analysis of Expressed Sequence Tag (EST) abundance led to the discovery of a number of previously uncharacterized genes that are expressed in the HN1 variety but are completely absent from the HM1 and HT1 EST libraries ( Fig. 1B ). (ampliconexpress.com)
  • PCR analysis revealed that the genes exclusively expressed in the HN1 variety are present as expected in the genome of HN1 but absent from the genomes of the HM1 and HT1 varieties ( Fig. 1B and fig. S6). (ampliconexpress.com)
  • cDNA expression library immunization (ELI) and analysis of expressed sequenced tags (EST) in a mouse model of tick infestations was used to identified cDNA clones that affected I. scapularis. (science-bbs.com)
  • The tissue specific expression analysis by using quantitative RT-PCR assays indicated that AhLPAT was ubiquitously expressed in root, stem, leaf, flower, gynophore and seed of peanut with the highest level in gynephore and seed. (chinacrops.org)
  • The most striking difference between JAK3 and the other JAKs was the presence of 2 stretches of additional amino acid sequences of 147 and 28 residues which spanned between amino acid positions 322 to 469 and 632 to 660, respectively. (appliedbioinfo.com)
  • A: An alignment of amino acid sequences of rat preproapelin with human and bovine preproapelin. (phoenixpeptide.com)
  • B: An alignment of amino acid sequences of human apelin and angiotensin II. (phoenixpeptide.com)
  • BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR primers design. (biomedcentral.com)
  • These unresolved questions served as motivation for the current phylogenetic analyses that are based on broad taxon sampling, substantially more nuclear genes (available through expressed sequence tag (EST) or complete genome projects), and comparative analyses of nuclear and mitochondrial gene datasets. (biomedcentral.com)
  • Of the 233 randomly selected clones, 25 were identified as differentially expressed genes between 5MT resistant and 5MT sensitive wild type plants. (korea.ac.kr)
  • Many of the novel cDNA sequences that were highly represented in the library showed a relative specificity to β-cells compared with other tissues, including glucagonoma, liver, kidney, brain, 3T3 fibroblasts, and AtT20 corticotrophs, and warrant further investigation. (diabetesjournals.org)
  • Sequence based assays will be developed following the creation of cDNA libraries from selected tissues of A. senegal. (europa.eu)
  • Trout TNFSF 13b RNA is expressed in immune tissues including the spleen, anterior kidney, and peripheral blood leukocytes but not in the liver. (usda.gov)
  • All three antigens were expressed in all I. scapularis stages and localized in {*filter*} tick tissues. (science-bbs.com)
  • The high-complexity cDNA libraries are being built from tissues collected in New Brunswick and Newfoundland, and individuals from the same populations have also been used to generate families for selective breeding. (canada.ca)
  • These tag-based technologies, which do not require a priori knowledge of genomic sequence, are well-suited for transcriptional profiling. (biomedcentral.com)
  • The sequence of AhLPAT cDNA was 1 629 bp, and its genomic sequence was 5 331 bp. (chinacrops.org)
  • Targeted integration by homologous recombination enables in-situ tagging and replacement of genes in the marine microeukaryote Diplonema papillatum . (umontreal.ca)
  • Construction of cDNA libraries from Protists and Fungi. (umontreal.ca)
  • In a more recent phylogenetic investigation with four nuclear gene sequences (EF-1α, HSP70, actin and β-tubulin), nucleariids associate confidently with Fungi, but only when selecting two slow-evolving chytridiomycetes [ 18 ]. (biomedcentral.com)
  • Some of these sequences could be assembled into larger composite sequences (termed contigs) based on overlapping sequence identity while other sequences had no overlapping sequence identity with any other members of the database and remained as unassembled singletons. (usda.gov)
  • Sequences were assembled into a database of assembled contigs and singletons and used to search public protein databases and annotate the sequences. (usda.gov)
  • The full database consists of 6,076 contigs and 58,221 singletons assembled from both the traditional EST and 454 sequences. (usda.gov)
  • A polymerase chain reaction-based subtractive hybridization procedure was applied to cDNAs prepared from mouse insulinoma (βTC3) and glucagonoma (αTC2) cell lines to construct a library of cDNAs that are highly expressed in pancreatic β-cells. (diabetesjournals.org)
  • A cDNA library of Chinese wild Vitis amurensis , which is the most cold-resistant species in the genus Vitis , was constructed using young leaves of seedlings of the clone Heilongjiang potted and subjected to cold stress. (geneticsmr.com)
  • RESULTS: Here, we report the characterization of a cDNA, 1RT126I22, which contains a TNF homology domain. (usda.gov)
  • Characterization of three Ixodes scapularis cDNAs protective against tick infestations. (science-bbs.com)
  • The cDNA for bovine IF2 mt was expressed in Escherichia coli under the control of the T7 polymerase promoter in a vector that provides a His 6 -tag at the C-terminus of the expressed protein. (elsevierpure.com)
  • We utilized a novel high throughput sequencing technology called 454 pyrosequencing which produced approximately 300,000 independent sequences. (usda.gov)
  • These 4 cDNA samples were used for 454 pyrosequencing which produced approximately 300,000 independent sequences. (usda.gov)
  • Over 300,000 putative SNPs have been identified, of which over 48,000 are high quality SNPs as defined by contig size of at least four sequences and the minor allele presence of at least twice in the contig. (auburn.edu)
  • Comparison of cDNA data from three aphid lineages identified single nucleotide polymorphisms that can be used as genetic markers and, in some cases, may represent functional differences in the protein products. (nih.gov)
  • Sequence Alignment: MSA using conserved domain and local sequence similarity information, COBALT, Protein sequence alignment, Nucleotide sequence alignment. (cutm.ac.in)
  • Aphids for library construction were raised on Arabidopsis thaliana, Nicotiana benthamiana, Brassica oleracea, B. napus, and Physalis floridana (with and without Potato leafroll virus infection). (nih.gov)
  • In particular, non-conservative amino acid substitutions in a highly expressed gut protease may be of adaptive significance for M. persicae feeding on different host plants. (nih.gov)
  • Genes known to be highly expressed in β-cells were represented at a high frequency, namely insulin (15 of 80 clones), islet amyloid polypeptide (8 of 80 clones), proinsulin convertase 1 (6 of 80 clones), and neuropeptide Y (2 of 80 clones). (diabetesjournals.org)
  • Transcription profiling revealed that nine GhTUBs were highly expressed in elongating fibre cells as compared with fuzzless-lintless mutant ovules. (singerinstruments.com)
  • Here we performed mRNA profiling using Massively Parallel Signature Sequencing (MPSS) and combined it with available Expressed Sequence Tag (EST) data. (biomedcentral.com)
  • Each sequence from this database was used to search public protein databases to assign putative function to as many database entries as possible. (usda.gov)
  • The first rainbow trout repeat elements database (INRA RT rep1.0) containing 735 putative repeat elements was developed, and identified almost 59.5% of the BES database in base-pairs as repetitive sequence. (biomedcentral.com)
  • The phylum-level affiliations of 93 16S rRNA sequences corresponded well with two taxonomically distinct EST patterns. (mpg.de)
  • A total of 6,528 clones were sequenced from this library generating 5,542 high-quality EST sequences. (nih.gov)
  • In 2008, total world production was about 576,000 metric tons with a total export value estimated around 2.4 billions USD ( http://www.fao.org/fishery/statistics/en ). (biomedcentral.com)
  • In this project, a total of 12 cDNA libraries were constructed including eight from channel catfish (Ictalurus punctatus) and four from blue catfish (I. furcatus). (auburn.edu)
  • A total of 1,960 nonredundant sequences (NRSs) were generated for N. oculata clone CS-179. (academicconcepts.net)
  • However, large-scale expressed sequence tag (EST) resources have been lacking for this species. (nih.gov)
  • In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents. (biomedcentral.com)
  • The H. scandens genome has a high overall repetitive sequence composition, 68.30% in the female and 66.78% in the male genome, with abundant long terminal repeat (LTR) retrotransposons (RTs), including more Ty3/Gypsy than Ty1/Copia elements, particularly two Ty3/Gypsy lineages, Tekay and Retand. (bvsalud.org)
  • Two microbial cDNA libraries were constructed from composite samples using semi-randomly primed RT-PCR. (mpg.de)
  • Some functional genes identified from the cDNA library have potential for plant defense. (geneticsmr.com)
  • The number and relative abundance of transcripts from stage II grape berries was defined using Massively Parallel Signature Sequencing (MPSS). (biomedcentral.com)
  • Of these unique sequences, over 35% had significant similarities to known genes by BLASTX searches, which allowed the identification of 14,776 unique genes in the catfish. (auburn.edu)
  • This large scale EST sequencing project would allow the identification of majority of catfish transcriptome. (auburn.edu)
  • Expressed sequence tags assigned to Alpha- and Betaproteobacteria were predominantly found in the oxic zone, while those affiliated with Deltaproteobacteria were more frequently detected in the anoxic zone. (mpg.de)
  • It is predominantly expressed in immune cells and transduces a signal in response to its activation via tyrosine phosphorylation by interleukin receptors. (appliedbioinfo.com)
  • A high quality normalized cDNA library was constructed. (nih.gov)
  • We performed Roche 454 pyrosequencing on cDNA libraries derived from stem and capsule tissue from all three varieties. (ampliconexpress.com)
  • The expressed protein has a number of degradation products in partially purified preparations and this factor is then further purified by high-performance liquid chromatography or gravity chromatography on anion exchange resins. (elsevierpure.com)
  • On sequence level, we are investigating the evolution of short linear motifs in proteins (SLiMs) and look specifically at predatory, as well as mechano-sensing motifs (in collaboration with the team of Tam Mignot). (univ-amu.fr)
  • We identified zebrafish and Fugu TNFSF 13b homologues by genomic DNA database searches and determined that the predicted proteins share 68% and 76% sequence identity with trout TNFSF 13b. (usda.gov)