Sequencing libraries expressed sequence tags. Medical search. Frequent questions

Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). (nih.gov)
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)
ESTs may be used to identify gene transcripts, and were instrumental in gene discovery and in gene-sequence determination. (wikipedia.org)
Because these clones consist of DNA that is complementary to mRNA, the ESTs represent portions of expressed genes. (wikipedia.org)
Because of the way ESTs are sequenced, many distinct expressed sequence tags are often partial sequences that correspond to the same mRNA of an organism. (wikipedia.org)
When the complete genome sequence of an organism is available and transcripts are annotated, it is possible to bypass contig assembly and directly match transcripts with ESTs. (wikipedia.org)
The more recent duplication event in particular would be expected to result in many paralogous pairs of genes differing by relatively few sequence differences, thus complicating gene identification using ESTs. (biomedcentral.com)
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)
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)
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)
Analysis of 20,257 high-quality ESTs yielded 6372 unique genes comprised of 3059 tentative consensus (TC) sequences and 3313 singletons (available at http://aksoylab.yale.edu ). (umd.edu)
Researchers sequenced an unfiltered genomic shotgun (trs) and a methylation-filtration (tmf) library of A. tauschii, and analyzed wheat expressed sequence tags (ESTs) to estimate the expression of genes and transposable elements (TEs). (harvard.edu)
cDNAs averaged 500-600 bp in length and were treated as expressed sequence tags (ESTs). (mpg.de)
National Centre for Biotechnology Information (NCBI): cDNA libraries and Expressed Sequence Tags (ESTs), EST analysis, Pairwise alignment techniques, Multiple sequence alignment. (cutm.ac.in)
Expressed sequenced tags (ESTs) of 1 019 randomly selected clones were analyzed and then assembled 588 unigens. (korea.ac.kr)

Through the Community Sequencing Program, a catfish EST sequencing project was selected by the DOE's Joint Genome Institute (JGI). (auburn.edu)

EST approaches have largely been superseded by whole genome and transcriptome sequencing and metagenome sequencing. (wikipedia.org)

Such EST data form a valuable foundation for the understanding of the gene composition and genomic biology of yet-to-be fully sequenced genomes [ 3 ]. (biomedcentral.com)
However, when applying this concept to genomes of multicellular organisms such as mammals, one has to deal with a large number of false positive predictions since many transcription factor genes are only expressed in specific tissues or cell types. (lu.se)
In 2006, the Joint Genome Institute completed low coverage survey sequencing of the genomes of five phenotypically and ecologically diverse Lake Malawi species. (biomedcentral.com)

The cDNAs used for EST generation are typically individual clones from a cDNA library. (wikipedia.org)
In 1982, the idea of selecting random or semi-random clones from such a cDNA library for sequencing was explored by Greg Sutcliffe and coworkers. (wikipedia.org)
sequenced 178 clones from a rabbit muscle cDNA library. (wikipedia.org)
Approximately 5,400 clones from each library were sequenced from both the 5' and 3' directions. (usda.gov)
Random Expressed Sequence Tag (EST) clones have been isolated and sequenced from dolphin Peripheral Blood Leukocyte (PBL) cDNA libraries. (vin.com)
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)
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)
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)

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)
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)
These analyses have also helped identify genes that were differentially expressed in DED fungi grown under defined experimental conditions. (sisef.it)

In 1991, Adams and co-workers coined the term EST and initiated more systematic sequencing as a project (starting with 600 brain cDNAs). (wikipedia.org)
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)
Of these, 17 were identical or homologous to known mammalian cDNAs or expressed sequence tags. (diabetesjournals.org)
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived. (ouhsc.edu)

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)
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)

Sequence Alignment: MSA using conserved domain and local sequence similarity information, COBALT, Protein sequence alignment, Nucleotide sequence alignment. (cutm.ac.in)
Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. (bvsalud.org)

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)

Soybean has a large (1115 Mbp) genome that has yet to be fully sequenced. (usda.gov)

Large scale gene analysis of most organisms is hampered by incomplete genomic sequences. (usda.gov)
The prediction of transcription factor binding sites in genomic sequences is in principle very useful to identify upstream regulatory factors. (lu.se)

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)
Functional annotation of gene sequences indicate functional classifications are not randomly distributed among gene families containing few or many genes. (usda.gov)

In an effort to reduce the number of expressed sequence tags for downstream gene discovery analyses, several groups assembled expressed sequence tags into EST contigs. (wikipedia.org)
BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR primers design. (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)
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)
2003. Comparative analyses of potato expressed sequence tag libraries . (berkeley.edu)
Here, we report computational and comparative analyses of survey sequence data to address the question of diversity. (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)

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)

Expression analysis of the three yolk proteins indicates that all are detected in females, while only the yolk protein with similarity to lipases, is expressed in males. (umd.edu)
When the background expectation is similarity, how does one use low coverage genome sequencing to detect that which makes organisms distinct? (biomedcentral.com)

This large scale EST sequencing project would allow the identification of majority of catfish transcriptome. (auburn.edu)

Expressedsequence tags, which map across intron-exon boundaries (around 300), indicate possible alternative splice sites,while expressed sequence tags, which map near the ends of known transcripts (around 600), suggest extensionof the coding or untranslated regions. (sfu.ca)

Many EST libraries were constructed from RNA extracted from various genetic backgrounds, thus gene identification from these sources is complicated by the existence of both gene and allele sequence differences. (usda.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)

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)

We provide a method to simultaneously screen a library of antibody fragments for binding affinity and cytoplasmic solubility by using the Escherichia coli twin-arginine translocation pathway, which has an inherent quality control mechanism for intracellular protein folding, to display the antibody fragments on the inner membrane. (jove.com)

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)
Analysis of these sequences revealed single base substitutions and single base indels are the most frequently observed form of sequence variation between genes within families in the dataset. (usda.gov)
In: Expressed sequence tags - generation and analysis, Methods in Molecular Biology Vol. 533 (J. Parkinson, ed. (umontreal.ca)
We developed TS-REX, a database/software system that supports the analysis of tissue and cell type-specific transcription factor-gene networks based on expressed sequence tag abundance of transcription factor-encoding genes in UniGene EST libraries. (lu.se)
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)
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 many organisms, such as soybean, the best source of sequence information is the existence of expressed sequence tag (EST) libraries. (usda.gov)

Targeted integration by homologous recombination enables in-situ tagging and replacement of genes in the marine microeukaryote Diplonema papillatum . (umontreal.ca)

The phylum-level affiliations of 93 16S rRNA sequences corresponded well with two taxonomically distinct EST patterns. (mpg.de)

They may be represented in databases as either cDNA/mRNA sequence or as the reverse complement of the mRNA, the template strand. (wikipedia.org)

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)

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)

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)

A first challenge is that tissue provenance of EST libraries is described in plain English in dbEST. (wikipedia.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)

DNA Data Bank of Japan (DDBJ): Sequence Alignment Methods, Predictive Methods Using DNA Sequences. (cutm.ac.in)
Commonly used methods for the display and screening of recombinant antibody libraries do not incorporate intracellular protein folding quality control, and, thus, the antigen-binding capability and cytoplasmic folding and solubility of antibodies engineered using these methods often must be engineered separately. (jove.com)

The identification of potential gene sequences (pHaps) from soybean allows us to begin to get a picture of the genomic history of the organism as well as begin to observe the evolutionary fates of gene copies in this highly duplicated genome. (usda.gov)

In 1979, teams at Harvard and Caltech extended the basic idea of making DNA copies of mRNAs in vitro to amplifying a library of such in bacterial plasmids. (wikipedia.org)
These approaches commonly use phage display, yeast surface display, or bacterial surface display to screen large libraries of antibodies 11-13 . (jove.com)

Sequence based assays will be developed following the creation of cDNA libraries from selected tissues of A. senegal. (europa.eu)

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 genetics, an expressed sequence tag (EST) is a short sub-sequence of a cDNA sequence. (wikipedia.org)

When available, the information provided by whole-genome sequencing projects provides an entry into an understanding of genome structure and evolution and gene discovery, and function. (biomedcentral.com)
Expressed Sequence Tag (EST) sequencing is one of the most efficient means for gene discovery and gene expression profiling. (auburn.edu)

We are also interested in evolutionary computational biology on sequence, cellular, and organismal level. (univ-amu.fr)

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)
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)

A collection of different allotypes or allelic protein variants, a new type of protein library. (genomicglossaries.com)
Using human coagulation factor IXa (fIXa) as a model system, we computationally screened 158 positions and expressed 98 variants to test experimentally for epitope mapping. (bvsalud.org)

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)

Over-expressed MS1 co-localized with actin in H9c2 cells and altered expression of genes of the myocardin-related transcription factor (MRTF)/serum response factor (SRF) transcriptional pathways and in addition the apoptosis repressor with caspase recruitment domain (Nol3) gene. (westminster.ac.uk)

Low coverage sequencing is now a routine strategy to uncover functional or 'constrained' genomic elements [ 30 ]. (biomedcentral.com)

Conserved Domains is a database of protein domains represented by sequence alignments and profiles for protein domains conserved in molecular evolution. (nih.gov)
This study examined potential gene sequences identified in EST libraries of soybean and assigned the potential gene sequences with molecular functions. (usda.gov)

Nuclear genome sequence and gene expression of an intracellular fungal endophyte stimulating the growth of cranberry plants. (umontreal.ca)
The method harnesses the intrinsic intracellular folding quality control mechanism of the Escherichia coli twin-arginine translocation (Tat) pathway to display an scFv library on the E. coli inner membrane. (jove.com)

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)

Expressed Sequence Tags" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (ouhsc.edu)

The resulting sequence is a relatively low-quality fragment whose length is limited by current technology to approximately 500 to 800 nucleotides. (wikipedia.org)
RESULTS: We identified approximately 45,000 potential gene sequences (pHaps) from EST sequences of Williams/Williams82, an inbred genotype of soybean (Glycine max L. Merr. (usda.gov)
Genomic sequencing of selected loci indicate that intron-like intervening sequences are numerous and are approximately 220 bp in length. (usda.gov)
Approximately 55% of the BES reads (97,846) had more than 100 base pairs of contiguous non-repetitive sequences. (biomedcentral.com)

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)

This makes it difficult to write programs that can unambiguously determine that two EST libraries were sequenced from the same tissue. (wikipedia.org)
To develop a foundation for tsetse physiology, a normalized expressed sequence tag (EST) library was constructed from fat body tissue of immune-stimulated Glossina morsitans morsitans. (umd.edu)

A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)
00:06:29 We call on all countries to increase the sequencing of the virus to supplement ongoing surveillance, monitoring and testing efforts and to share that data internationally. (bvsalud.org)

Anatomy5

Organisms7

Chemicals and Drugs22

Analytical, Diagnostic and Therapeutic Techniques and Equipment28

Phenomena and Processes58

Disciplines and Occupations2

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture4

Information Science30

Health Care4

ESTs19

Community Sequencing Program1

Superseded by whole genome1

Genomes3

Clones8

Differentially expressed3

CDNAs4

Protein sequences2

Nucleotide2

CDNA sequences1

Fully sequenced1

Genomic sequences2

Annotation2

Analyses6

Contigs3

Unique sequences1

Similarity2

Transcriptome1

Transcripts1

Allele sequence1

Unigenes1

300,0002

Antibody fragments1

Analysis6

Organisms1

Homologous1

Distinct1

MRNA1

Fungi2

Predominantly2

Species1

DbEST1

Microarray1

Methods2

Identification1

Bacterial2

Tissues1

Arabidopsis1

Genetics1

Gene discovery2

Computational Biology1

Databases2

Variants2

Substitutions1

Transcriptional1

Functional1

Molecular2

Intracellular2

Patterns1

MeSH1

Approximately4

Amino acid1

Tissue2

Data2