81,184 research outputs found
Data Mining for Simple Sequence Repeats in Oil Palm Expressed Sequence Tags
No full textExpressed Sequence Tags or ESTs are small pieces of DNA sequence that are generated by sequencing either one or both ends of an expressed gene. ESTs provide researchers with a quick and inexpensive route for discovering new genes, for obtaining data on gene expression and regulation, and for constructing genome maps. Oil palm EST sequences as available in public domain are downloaded. They were grouped and made contigs using CAP3 and Phrap. Microsatellite repeats are located using 5 softwares (MISA, TRA, TROLL, SSRIT, SSR primer). Among the 5 methods MISA is found to be the best. It can elucidate the compound repeat also. Frequency and total number (202) of SSR were detected. Mononucleotide repeat is more abundant especially ‘A/T’ repeats in Oil palm. Flanking primers were designed using primer3, SSR primers. The results of the study are given as an online database ‘MEMCO’ to help Oil palm researchers
prot4EST: translating expressed sequence tags from neglected genomes
No full textThe genomes of an increasing number of species are being investigated through generation of expressed sequence tags (ESTs). However, ESTs are prone to sequencing errors and typically define incomplete transcripts, making downstream annotation difficult. Annotation would be greatly improved with robust polypeptide translations. Many current solutions for EST translation require a large number of full-length gene sequences for training purposes, a resource that is not available for the majority of EST projects
200 000 nematode expressed sequence tags on the Net
No full textExpressed sequence tags (ESTs) are single-pass sequence reads made from randomly selected cDNA clones, which represent the expressed genes of an organism. EST analysis is an efficient and cost-effective method for sampling the genes expressed by an organism or tissue. ESTs have been a focus of eukaryotic parasite genome initiatives for several years 1 (see the Parasite Genome web server at http://www.ebi.ac.uk/parasites/parasite-genome.html), and parasitic organism ESTs make up a significant portion of the dbEST subsection of GenBank 2 , 3 . EST data sets can be mined for useful or interesting content using standard similarity-based search tools such as BLAST. In the field of molecular parasitology, such approaches have led to the discovery of many new potential drug targets and vaccine candidates. However, EST data sets also contain important additional types of information
An expressed sequence tag survey of gene expression in the pond snail Lymnaea stagnalis, an intermediate vector of Fasciola hepatica
No full textThe pond snail Lymnaea stagnalis is an intermediate vector for the liver fluke Fasciola hepatica, a common parasite of ruminants and humans. Yet, despite being a disease of medical and economic importance, as well as a potentially useful comparative tool, the genetics of the relationship between Lymnaea and Fasciola has barely been investigated. As a complement to forthcoming F. hepatica expressed sequence tags (ESTs), we generated 1320 ESTs from L. stagnalis central nervous system (CNS) libraries. We estimate that these sequences derive from 771 different genes, of which 374 showed significant similarity to proteins in public databases, and 169 were similar to ESTs from the snail vector Biomphalaria glabrata. These L. stagnalis ESTs will provide insight into the function of the snail CNS, as well as the molecular components of behaviour and response to parasitism. In the future, the comparative analysis of Lymnaea/Fasciola with Biomphalaria/Schistosoma will help to understand both conserved and divergent aspects of the host-parasite relationship. The L. stagnalis ESTs will also assist gene prediction in the forthcoming B. glabrata genome sequence. The dataset is available for searching on the world-wide web at http://zeldia.cap.ed.ac.uk/mollusca.html
An Expressed Sequence Tag Analysis of the Intertidal Brown Seaweeds Fucus serratus (L.) and F. vesiculosus (L.) (Heterokontophyta, Phaeophyceae) in Response to Abiotic Stressors
No full textPearson GA, Hoarau G, Lago-Leston A, et al. An Expressed Sequence Tag Analysis of the Intertidal Brown Seaweeds Fucus serratus (L.) and F. vesiculosus (L.) (Heterokontophyta, Phaeophyceae) in Response to Abiotic Stressors. Marine Biotechnology. 2009;12(2):195-213.In order to aid gene discovery and uncover genes responding to abiotic stressors in stress-tolerant brown algae of the genus Fucus, expressed sequence tags (ESTs) were studied in two species, Fucus serratus and Fucus vesiculosus. Clustering of over 12,000 ESTs from three libraries for heat shock/recovery and desiccation/rehydration resulted in identification of 2,503, 1,290, and 2,409 unigenes from heat-shocked F. serratus, desiccated F. serratus, and desiccated F. vesiculosus, respectively. Low overall annotation rates (18–31%) were strongly associated with the presence of long 3' untranslated regions in Fucus transcripts, as shown by analyses of predicted protein-coding sequence in annotated and nonannotated tentative consensus sequences. Posttranslational modification genes were overrepresented in the heat shock/recovery library, including many chaperones, the most abundant of which were a family of small heat shock protein transcripts, Hsp90 and Hsp70 members. Transcripts of LI818-like light-harvesting genes implicated in photoprotection were also expressed during heat shock in high light. The expression of several heat-shock-responsive genes was confirmed by quantitative reverse transcription polymerase chain reaction. However, candidate genes were notably absent from both desiccation/rehydration libraries, while the responses of the two species to desiccation were divergent, perhaps reflecting the species-specific physiological differences in stress tolerance previously established. Desiccation-tolerant F. vesiculosus overexpressed at least 17 ribosomal protein genes and two ubiquitinribosomal protein fusion genes, suggesting that ribosome function and/or biogenesis are important during cycles of rapid desiccation and rehydration in the intertidal zone and possibly indicate parallels with other poikilohydric organ organisms such as desiccation-tolerant bryophytes
Expression of CYP71B7, a cytochrome P450 expressed sequence tag from Arabidopsis thaliana
No full textThe systematic sequencing of anonymous cDNA clones (expressed sequence tags or ESTs) from the plantArabidopsis thalianahas identified a number of cDNAs with similarity to known cytochrome P450 sequences. The partial sequence of one of these cDNAs, 5G6, indicated that it was likely to encode a full-length cytochrome P450 monooxygenase (cyt P450) sequence. In this paper we describe the complete sequence of this clone, which has been designatedCYP71B7in accordance with the nomenclature for the cyt P450 gene superfamily. The cDNA was used to determine the pattern of expression of the corresponding gene inA. thaliana.Northern hybridization analysis indicated that maximal expression ofCYP71B7occurred in rosette leaves. Weaker hybridizing bands were also detected by Northern analysis of RNA from roots, leaves, flowers, and siliques. No expression could be detected in stem tissue. Southern analysis indicated that theCYP71B7gene was likely to exist as a single copy in the genome ofA. thaliana. CYP71B7was expressed episomally in yeast, and microsomes prepared from transgenic yeast exhibited a carbon monoxide difference spectrum characteristic of cyt P450. Microsomes from yeast expressingCYP71B7were assayed for enzymatic activity with synthetic model cyt P450 substrates. Microsomes from yeast cells expressingCYP71B7or those from control cells exhibited no detectable NADPH-supported 7-ethoxycoumarin or 7-ethoxyresorufin deethylase activities. However, in the presence of cumene hydroperoxide, activity was observed with microsomes from cells expressing CYP71B7 with 7-ethoxycoumarin as substrate. Organic hydroperoxides are well known to support cyt P450 catalysis in the absence of electrons from NADPH. The yeast microsomes contained high levels of endogenous NADPH–ferricytochrome P450 reductase (CPR) activity. The data suggest that thisA. thalianacyt P450, although expressed in an active form, is incapable of accepting electrons from the endogenous yeast CPR protein
Design and Implementation of Expressed Sequence Tag Alignment Tool
No full text[[abstract]]This thesis is to design the software, which can align the sequence of Express Sequence Tags database to its own genome. The main way is to implement Multi-Layer Unique Makers table, and use the concept of grid to reach distributed computing. The purpose is to analyze large amount of Express Sequence Tags in a personal computer, and produce important information that is relevant. Also to allow biologists and researchers who are in the field of bio-informatics to acquire the information they need within a lower budget.
In the recent years, a tremendous amount of DNA sequence information has been developed by molecule bio-labs from the entire world. Since BLAST was published in 1990, almost all the bio-information problems depended on the use of it. However, the speed of managing this information still needed to be emphasized. Therefore, many ideas were brought up to improve the old way. The key points of the new software for the biologists are not only to improve the speed on problem solving, but also on the accuracy.
This thesis is trying to emphasize this kind of demand. It will allow biologists to find out the gene sequences and gene structures much quicker and correct. It will also become the public open basis for Express Sequence Tags analysis
Making sense of EST sequences by CLOBBing them
No full textAbstract Background Expressed sequence tags (ESTs) are single pass reads from randomly selected cDNA clones. They provide a highly cost-effective method to access and identify expressed genes. However, they are often prone to sequencing errors and typically define incomplete transcripts. To increase the amount of information obtainable from ESTs and reduce sequencing errors, it is necessary to cluster ESTs into groups sharing significant sequence similarity. Results As part of our ongoing EST programs investigating 'orphan' genomes, we have developed a clustering algorithm, CLOBB (Cluster on the basis of BLAST similarity) to identify and cluster ESTs. CLOBB may be used incrementally, preserving original cluster designations. It tracks cluster-specific events such as merging, identifies 'superclusters' of related clusters and avoids the expansion of chimeric clusters. Based on the Perl scripting language, CLOBB is highly portable relying only on a local installation of NCBI's freely available BLAST executable and can be usefully applied to > 95 % of the current EST datasets. Analysis of the Danio rerio EST dataset demonstrates that CLOBB compares favourably with two less portable systems, UniGene and TIGR Gene Indices. Conclusions CLOBB provides a highly portable EST clustering solution and is freely downloaded from: http://www.nematodes.org/CLOBB</p
Expressed sequence tag survey of gene expression in the scab mite Psoroptes ovis--allergens, proteases and free-radical scavengers
No full textPsoroptes ovis, the causative agent of sheep scab, is an important ectoparasitic mite infecting sheep, goats and cattle. Infection is characterized by an extensive dermatitis, scab formation and intense itching. Initial focal lesions spread outwards, coalesce and may extend over the whole body. The host response to infestation has all the characteristics of an immediate-type hypersensitivity reaction but the mite antigens and allergens which initiate this response are almost completely undefined. Here, 507 randomly selected cDNAs derived from a mixed population of P. ovis were sequenced and the resultant nucleotide sequences subjected to Cluster analysis and Blast searches. This analysis yielded 280 clusters of which 49 had > 1 sequence with 24 showing significant Blast X homology to another protein in the databases. There were 231 sequences which appeared on one occasion and 109 of these showed significant Blast X homology to other sequences in the databases. This analysis identified homologues of 9 different types of allergens which have been characterized in other allergic conditions such as responses to house dust mites. It also identified a number of cysteine proteases which may contribute to lesion development as well as several free-radical scavenging enzymes which may protect the mite from host immune effector responses
Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensis and the evolution of secreted proteins in parasites
No full textParasitism is a highly successful mode of life and one that requires suites of gene adaptations to permit survival within a potentially hostile host. Among such adaptations is the secretion of proteins capable of modifying or manipulating the host environment. Nippostrongylus brasiliensis is a well-studied model nematode parasite of rodents, which secretes products known to modulate host immunity
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