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Topic: Expressed sequence tags

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	Expressed sequence tag (Site not responding. Last check: 2007-11-01)
		An expressed sequence tag or EST is a short sub-sequence of a protein -coding DNA sequence.
		An EST is produced by one-shot sequencing of a cloned mRNA, and the resulting sequence is a relatively low quality fragment whose length is limited by current technology to approximately 500 to 800 nucleotide s.
		ESTs are also a useful resource for designing probes for microarray s used to determine gene expression.
	www.serebella.com /encyclopedia/article-Expressed_sequence_tag.html (1285 words)

	Expressed sequence tag in TutorGig Encyclopedia (Site not responding. Last check: 2007-11-01)
		An 'expressed sequence tag' or 'EST' is a short sub-sequence of a transcribed protein-coding or non-protein-coding DNA sequence.
		Then the investigator can search for sequence similarity between DNA sequences in a region of interest and ESTs known to be located in the same region (and possibly known to be expressed in a tissue that would be consistent with the disease in question).
		ESTs are also a useful resource for designing probes for DNA microarrays used to determine gene expression.
	www.tutorgig.com /ed/expressed_sequence_tag (381 words)

	Pig EST database (Site not responding. Last check: 2007-11-01)
		The similarity among the EST sequences and pig gene sequences was also determined by BLAST alignment against 2,011 pig gene sequences from Genbank.
		The EST sequences were obtained from porcine whole embryo, term placenta, anterior pituitary, hypothalamus and ovary.
		The new version of pig EST database accomomdates 98,988 pig ESTs which were obtained from NCBI dbEST database, the BLAST alignment data, associated Human UniGene and RH maps (EBI GenomeMap'99, NCBI GeneMap'99), Pig-Human Comparative Map information and mapped pig genes in the pig genome database (PIGBASE).
	pigest.genome.iastate.edu /index.html (209 words)

	TIGR Gene Indices Information Page
		Expressed Sequence Tags are partial, single-pass sequences from either end of a cDNA clone.
		Sequences were either loaded directly from GenBank (cDNAs) or were derived from genomic sequences.
		All sequences from the appropriate division of GenBank were extracted.
	www.tigr.org /tdb/tgi/definitions.html (589 words)

	Trees and flowers more akin than dissimilar
		Homology of expressed genes in loblolly pine and Arabidopsis thaliana
		And yet, based on their analysis of more than 60,000 expressed sequence tags, Sederoff said the team found that 90 percent of the sturdy pine's genes match those of the tiny herbaceous plant.
		This "substantial conservation of gene sequence in seed plants," despite 300 million years of evolution and adaptation, means that herbaceous plants have the genetic potential to produce wood, and that woody plants might be engineered for other favorable characteristics.
	www.eurekalert.org /pub_releases/2003-05/ncsu-taf052803.php (784 words)

	Genome Glossary
		This file describes the portion of the component sequence used in the contig, in addition to the location on the contig of the component sequence.
		This is the portion of an mRNA or genomic sequence that encodes for a protein sequence.
		If the sequence from one end is found in a particular sequence contig, and the sequence from the other end is found in a different sequence contig, the two sequence contigs are said to be linked.
	www.ncbi.nlm.nih.gov /genome/guide/glossary.htm (2674 words)

	Plenary Detail
		In 1990, he developed expressed sequence tags (ESTs), a new strategy for gene discovery that has revolutionized the biological sciences.
		Genome Sequence of the Lyme Disease Spitochaete, Borrelia burgdorferi.
		Sequence and Analysis of Chromosome 2 of Arabidopsis thaliana.
	www.sc2001.org /plenary_venter.html (585 words)

	NINDS Scientists Isolate Segments Of DNA Sequence That Identify More Than 2,300 Brain Genes: National Institute of ...
		The number of genes expressed in the brain may be as many as 30,000 of the body's approximately 50,000-100,000 genes.
		In studies to sequence the human genome, scientists typically decode a strip of DNA from the chromosomes within the cell's nucleus to get an ordered string of nucleic acid letters, or sequence.
		This sequence is comprehensive and includes a small proportion of code from genes located within a large amount of other genetic code, most of which has unknown function.
	www.ninds.nih.gov /news_and_events/press_releases/pressrelease_braingenes_021292.htm (983 words)

	Center for Medicago Genomics Research: ESTs
		The Medicago Genome Initiative (MGI) is an EST sequence database of the model legume M.
		EST clustering) sequences to interact with the same generalized relational database structure.
		The initial goal of the project was to generate an approximately one-fold whole genome shotgun sequence data of the 500 megabase genome from a plasmid-based genomic library and obtain target shotgun clones for additional primer walking-based sequencing.
	www.noble.org /medicago/EST.html (814 words)

	Ethan Frome (Site not responding. Last check: 2007-11-01)
		This database is based upon expressed sequence tags, or short sequences, which are a few hundred base pairs in length, which are derived by partial, single pass sequencing of the inserts of randomly selected cDNA clones (Adams et al, 1991).
		ESTs are also a rapid and efficient way of establishing a detailed profile of the genes expressed in a tissue or cell type.
		Sequence data were compared with EMBL including dbEST for identification using the Fasta program (http://www.menu.hgmp.mrc.ac.uk, access to fasta program).
	www.swan.ac.uk /cget/ejgt/Zheng_ESTpaper.htm (1454 words)

	Kinetoplastid Biology and Disease \| Full text \| Trypanosoma rangeliTranscriptome Project: Generation and analysis of ...
		The obtained sequences were edited and analyzed using the new ESTonSQL system under development in collaboration of D.M. Lorenzini with the UFSC Bioinformatics laboratory http://www.bioinformatica.ufsc.br.
		Along with the continuing EST generation by sequencing both ends of all obtained clones, ORESTES (ORF ESTs) profiles [17] will be obtained from the same libraries used for EST generation.
		While ESTs are generated by sequencing the 5' and/or 3' ends of cDNA clones, the ORESTES technique allows the generation of sequences belonging to the middle portion of the genes [17].
	www.kinetoplastids.com /content/3/1/1 (1550 words)

	NCBI dbEST
		A brief account of the history of human ESTs in GenBank is available (Trends Biochem.
		"Trace data" for sequences derived from I.M.A.G.E clones is available from the Washington University Genome Sequencing Center.
		The last 3 are used to indicate sequence tags for individual cDNA libraries which are included in a pooled library.
	www.ncbi.nlm.nih.gov /dbEST (225 words)

	Characterization of the human ABC superfamily: isolation and mapping of 21 new genes using the expressed sequence tags ...
		Such expressed sequence tags (ESTs) are useful for identifying new genes, as tools for genetic mapping, and for the analysis of gene expression (25).
		The results in Figure 2 show that the EST sequences contain conserved amino acids that are found in all known members of the gene family, but are distinct from all previously characterized genes.
		Sequences were read with an IBI Gel Reader and analyzed with the Genetics Computer Group package of programs (29) running on a VAX computer.
	hmg.oupjournals.org /cgi/content/full/5/10/1649 (5616 words)

	Characterization of Constitutive and Putative Differentially Expressed mRNAs by Means of Expressed Sequence Tags, ... (Site not responding. Last check: 2007-11-01)
		Three are putative differentially expressed cDNAs from blood fed and Leishmania-infected midgut, a chitinase, a V-ATPase and a MAP kinase.
		Even at the dawn of the XXI century leishmaniasis is still one of the most important tropical diseases in the world, afflicting countries located mostly in Latin America, Africa and Asia with approximately two million new cases every year (www.who.int/ctd/html).
		These strategies include expression of molecules that can be either specifically toxic to the parasite or which may be able to block the interaction of the parasite with the midgut epithelia, thus halting obligatory steps for parasite survival in the vector.
	memorias.ioc.fiocruz.br /961/4077.html (1041 words)

	Genome Biology \| Abstract \| Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus ...
		Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensis and the evolution of secreted proteins in parasites
		Among 1,234 ESTs, 197 (~16%) contain predicted 5' signal sequences, with 176 classified as conventional signal peptides and 21 as signal anchors.
		Of all novel sequences identified, 32% contained predicted signal peptides, whereas this was the case for only 3.4% of conserved genes with sequence homologies beyond the Nematoda.
	www.genomebiology.com /2004/5/6/R39/abstract (406 words)

	PG-II: ARABIDOPSIS THALIANA EXPRESSED SEQUENCE TAGS AND THEIR ANALYSIS (Site not responding. Last check: 2007-11-01)
		Using the sequences from the randomly picked clones, we have begun to design a data analysis system which will make this data and derived information available with a minimum of human intervention.
		To this end, we have developed mechanisms to analyze large numbers of sequences and parse the results of these analyses; a decision tree has been coded as an adjunct to a spreadsheet to summarize the parsed results of the analysis.
		To address the issues of how much sequence information is essential for inferring function from the current similarity algorithms, we have analyzed 3'-truncated ESTs in order to determine the minimal amount of sequence data necessary to retain similarity scoring capacity.
	www.intl-pag.org /2/abstracts/185pg2.html (355 words)

	Comparative analysis of expressed sequence tags from Sesamum indicum and Arabidopsis thaliana developing seeds. (Site not responding. Last check: 2007-11-01)
		ESTs were clustered and analyzed by the BLASTX or FASTAX program against the GenBank NR and Arabidopsis proteome databases.
		Analyses of these two seed EST sets have helped to identify similar and different gene expression profiles during seed development, and to identify a large number of sesame seed-specific genes.
		In particular, we have identified EST candidates for genes possibly involved in biosynthesis of sesame lignans, sesamin and sesamolin, and also suggest a possible metabolic pathway for the generation of cofactors required for synthesis of storage lipid in non-green oilseeds.
	www.plant-genomic-papers.com /1081161708/index_html (313 words)

	Gene Sequence Tags from Plasmodium falciparum Genomic DNA Fragments Prepared by the "Genease" Activity of Mung Bean ...
		Gene Sequence Tags from Plasmodium falciparum Genomic DNA Fragments Prepared by the "Genease" Activity of Mung Bean Nuclease -- Reddy et al.
		Analysis of gene sequence tags prepared from mung bean nuclease-digested Plasmodium falciparum DNA demonstrates that this method has several advantages over the popular cDNA expressed sequence tag approach.
		These gene sequence tags will form a useful data base from which to initiate projects to develop new therapeutics, vaccines, and strategies to control human malaria.
	www.pnas.org /cgi/content/abstract/90/21/9867 (462 words)

	BioMed Central \| Abstract \| Optimal cDNA microarray design using expressed sequence tags for organisms with limited ...
		Sequence similarity between ESTs, quantified by the E-value of pair-wise alignment, was used as a surrogate for expected hybridization between corresponding sequences.
		Using this value as a measure of dissimilarity, sequence redundancy reduction was performed by hierarchical cluster analyses.
		For a given stage in the agglomeration procedure, the EST having the highest similarity to all the other sequences within each cluster, the centroid EST, was selected as a microarray probe.
	www.biomedcentral.com /1471-2105/5/191/abstract (469 words)

	BioMed Central \| Abstract \| Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid ...
		A putative unigene set of 1304 sequences – 133 contigs and 1171 singlets – has been developed, and the transcripts have been functionally annotated.
		The ESTs have been functionally characterized and genes relevant to specific physiological processes of economic importance have been identified.
		Sequences derived from this effort may be used to speed gene discovery efforts in Fragaria and the Rosaceae in general and also open avenues of comparative mapping.
	www.biomedcentral.com /1471-2229/5/12/abstract (343 words)

	BRISTOL, UNITED KINGDOM
		This program has been applied initially to the >100 000 expressed maize sequences available in the public databases and will be used to identify putative polymorphisms within expressed sequences derived from the Bristol-based IGF program and other public wheat sequence repositories.
		Interestingly, the level of sequence variation within the flanking regions of microsatellites linked to expressed sequence tags appears to be lower than microsatellites that were unlinked to expressed sequence tags.
		The sequence information generated and the assay developed could be used as a starting point for the further development of a non-gel based, multi-locus, multi-allele screen for large-scale maize genotyping (Mogg et al.
	www.maizegdb.org /mnl/76/28edwards.html (588 words)

	Morton et al.: Chromosome 7 EST Mapping (Site not responding. Last check: 2007-11-01)
		Twenty-one putative chromosome 7-derived expressed sequence tags (ESTs) identified 33 yeast artificial chromosomes (YACs) or P1 clones, which were then used as reagents for physical mapping.
		FISH mapping established that the ESTs contained within these clones were distributed throughout chromosome 7, with all major cytogenetic bands represented, except 7p13-p15, 7p11,7q31.2, and 7q35.
		Each EST sequence identified at least one other sequence in publicly available databases (using search tools such as BLASTN, basic local alignment search tool), and many of the ESTs identified cDNAs and several genomic DNA sequences.
	www.genlink.wustl.edu /repository/abstracts/morton1-ab.html (228 words)

	The Schistosome Genome Project: RNA Arbitrarily Primed- PCR Allows the Accelerated Generation of Expressed Sequence Tags (Site not responding. Last check: 2007-11-01)
		These factors reduce the number of useful sequences obtained and thus increase the costs and the time required to tag all of the genes expressed by the parasite.
		The obtained sequences were initially edited in order to subtract both vector and primer sequences.
		The edited sequences were then submitted for analysis to the servers available at the National Center for Biotechnology Information, National Institutes of Health, USA and European Molecular Biology Laboratories, Heidelberg, Germany.
	memorias.ioc.fiocruz.br /915/3104.html (1750 words)

	Industry Programme
		The information in the EBI's database of expressed sequence tags - EMEST - is being made available through a CORBA service to improve access to these data.
		Expressed sequence tags (ESTs) are short (200-500bp) DNA sequences generated from the 3' and 5' ends of randomly selected cDNA clones.
		The purpose of EST sequencing is to rapidly scan for all the protein coding genes and to provide a "tag" for each gene on the genome.
	www.ebi.ac.uk /industry/Projects/projects.html (973 words)

	Fristensky et al. Expressed sequence tags from the defense response of Brassica napus to Leptosphaeria maculans. (Site not responding. Last check: 2007-11-01)
		Expressed sequence tags from the defense response of Brassica napus to Leptosphaeria maculans.
		The resultant Expressed Sequence Tags (ESTs) include sequences homologous to previously-identified defense genes, disease resistance genes, and stress-related genes, as well as genes involved in photosynthesis, metabolism and other functions not associated with defense.
		Because of the wide range of ESTs identified, it may also be useful in other systems, such as stress or light regulation.
	www.bspp.org.uk /mppol/abstract/0301fris.htm (218 words)

	Census of Genes Expressed in Porcine Embryos and Reproductive Tissues by Mining an Expressed Sequence Tag Database ...
		expressed in embryos and reproductive tissues in pigs.
		EST sequences derived from the pig embryos and reproductive
		Genes expressed in pig embryos and reproductive tissues on the Y chromosome
	www.biolreprod.org /cgi/content/full/69/4/1177 (3215 words)

	Expressed Sequence Tags (Site not responding. Last check: 2007-11-01)
		Expressed Sequence Tags (ESTs) are short DNA sequences, usually based on a single dideoxy sequencing run, representing sequences expressed in an organism under particular conditions.
		The sequences have been submitted to dbEST, a part of the GenBank database.
		ESTs from the basidiomycete Schizophyllum commune grown on nitrogen-replete and nitrogen-limited media.
	biology.semo.edu /agathman/lab/est.htm (201 words)

	TIGR Gene Indices Information Page
		Sequences were either loaded directly from GenBank (cDNAs) or were derived from genomic sequences when cDNAs were not available.
		Using the CAP3 Sequence Assembly Program sequences were assembled into contigs.
		TCs are consensus sequences based on two or more ESTs (and possibly an ET) that overlap for at least 40 bases with at least 95% sequence identity.
	www.tigr.org /tdb/tgi_info.html (647 words)

	Genome Biology \| Research news
		Now that we have the whole human genome sequence, the challenge remains to identify all the genes and transcripts hidden within it.
		This differs from the conventional expressed sequence tag (EST) strategy in that it provides sequence information along the whole length of each transcript, rather than just the ends.
		Shotgun sequencing of the human transcriptome with ORF expressed sequence tags.
	www.genomebiology.com /researchnews/default.asp?arx_id=gb-spotlight-20011011-01 (231 words)

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