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An optimized protocol for analysis of EST sequences 总被引:17,自引:1,他引:16
Liang F Holt I Pertea G Karamycheva S Salzberg SL Quackenbush J 《Nucleic acids research》2000,28(18):3657-3665
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Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species 总被引:6,自引:0,他引:6
Yuan Q Quackenbush J Sultana R Pertea M Salzberg SL Buell CR 《Plant physiology》2001,125(3):1166-1174
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Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index 总被引:4,自引:0,他引:4
TadS. Sonstegard Anthony V. Capuco Joseph White Curtis P. Van Tassell Erin E. Connor Jennifer Cho Razvan Sultana Larry Shade James E. Wray Kevin D. Wells John Quackenbush 《Mammalian genome》2002,13(7):373-379
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A hitchhiker's guide to expressed sequence tag (EST) analysis 总被引:3,自引:0,他引:3
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Expressed Sequence Tags (ESTs) are short, usually unedited sequences obtained by single-pass sequencing of cDNA clones from
any cDNA library. Analyzing and comparing ESTs can provide information on gene expression, function and evolution. Large-scale
EST sequencing has become an attractive alternative to plant genome sequencing. Currently, plant EST collections comprise
over 3.8 million sequences from about 200 species. They have proved to be a valuable tool for gene discovery and plant metabolism
analysis. Several plant-specific EST databases have been created which provide access to sequence data and bioinformatics-based
tools for data mining. Searching EST collections allows pre-selection of genes for preparing cDNA arrays, targeted to bring
maximum information on specialized processes, like stress response, symbiotic nitrogen fixation etc. Also, ESt-based molecular
markers such as SNP, SSR, and indels are fast developing tools for breeders and researchers. 相似文献
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A porcine BAC clone harboring the tightly linked IFNAR1 and IFNGR2 genes was identified by comparative analysis of the publicly available porcine BAC end sequences. The complete 168,835 bp insert sequence of this clone was determined. Sequence comparisons of the genomic sequence with EST sequences from public databases were performed and allowed a detailed annotation of the IFNAR1 and IFNGR2 genes. The analyzed genes showed a conserved genomic organization with their known mammalian orthologs, however the sequence conservation of these genes across species was relatively low. In addition to the IFNAR1 and IFNGR2 genes, which were completely sequenced, the analyzed BAC clone also contained parts of an orphan gene encoding a putative transmembrane protein (TMEM50B). In contrast to the IFNAR1 and IFNGR2 genes the sequence conservation of the TMEM50B gene across different mammalian species was extremely high. 相似文献
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Positional candidate gene selection from livestock EST databases using Gene Ontology 总被引:3,自引:0,他引:3
MOTIVATION: The number of expressed sequence tags (ESTs) in GenBank has now surpassed 200,000 for cattle and 100,000 for swine. The Institute of Genome Research (TIGR) has organized these sequences into approximately 60,000 non-redundant consensus sequences (identified by TIGR Gene Indices) for cattle and 40,000 for swine. Anonymous ESTs are of limited value unless they are connected to function. Functional information is difficult to manage electronically because of heterogeneity of meaning and form among databases. The Gene Ontology (GO) Consortium has produced ontologies for gene function with consistent meaning and form across species. Linking livestock EST to gene function through similarity with sequences from other annotation-rich mammals could accelerate: (1) the discovery of positional candidate genes underlying a livestock quantitative trait locus (QTL) and (2) comparative mapping between livestock and other mammals (e.g. humans, mouse and rat). We initiated this investigation to determine if incorporation of the GO into the annotation process could accelerate livestock positional candidate gene discovery. RESULTS: We have associated livestock ESTs with GO nodes through sequence similarity to the NCBI Reference Sequences (RefSeq). Positional candidate genes are identified within minutes that otherwise required days. The schema described here accommodates queries that return GO nodes from terms familiar to biologists, such as gene name, alternate/alias symbol, and OMIM phenotype. AVAILABILITY: Scripts and schema are available on request from the authors. 相似文献