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  • 1
    Language: English
    In: Plant physiology, October 2005, Vol.139(2), pp.610-8
    Description: PlantGDB (http://www.plantgdb.org/) is a database of plant molecular sequences. Expressed sequence tag (EST) sequences are assembled into contigs that represent tentative unique genes. EST contigs are functionally annotated with information derived from known protein sequences that are highly similar to the putative translation products. Tentative Gene Ontology terms are assigned to match those of the similar sequences identified. Genome survey sequences are assembled similarly. The resulting genome survey sequence contigs are matched to ESTs and conserved protein homologs to identify putative full-length open reading frame-containing genes, which are subsequently provisionally classified according to established gene family designations. For Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the exon-intron boundaries for gene structures are annotated by spliced alignment of ESTs and full-length cDNAs to their respective complete genome sequences. Unique genome browsers have been developed to present all available EST and cDNA evidence for current transcript models (for Arabidopsis, see the AtGDB site at http://www.plantgdb.org/AtGDB/; for rice, see the OsGDB site at http://www.plantgdb.org/OsGDB/). In addition, a number of bioinformatic tools have been integrated at PlantGDB that enable researchers to carry out sequence analyses on-site using both their own data and data residing within the database.
    Keywords: Databases, Genetic ; Genome, Plant ; Plants -- Genetics
    ISSN: 0032-0889
    E-ISSN: 15322548
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  • 2
    Language: English
    In: Genome biology, 2006, Vol.7(11), pp.R111
    Description: The eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, but the software supports inclusion of any property that can be associated with a genomic location. The xGDB distribution and user support utilities are available online at the xGDB project website, http://xgdb.sourceforge.net/.
    Keywords: Software ; Computational Biology -- Methods ; Genome -- Genetics ; Genomics -- Methods
    ISSN: 14656906
    E-ISSN: 1474-760X
    E-ISSN: 14656914
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  • 3
    Language: English
    In: Nucleic acids research, 01 January 2004, Vol.32(Database issue), pp.D354-9
    Description: PlantGDB (http://www.plantgdb.org/) is a database of molecular sequence data for all plant species with significant sequencing efforts. The database organizes EST sequences into contigs that represent tentative unique genes. Contigs are annotated and, whenever possible, linked to their respective genomic DNA. Genome sequence fragments are assembled similarly. The goal of the PlantGDB web site is to establish the basis for identifying sets of genes common to all plants or specific to particular species by integrating a number of bioinformatics tools that facilitate gene prediction and cross- species comparisons. For species with large-scale genome sequencing efforts, PlantGDB provides genome browsing capabilities that integrate all available EST and cDNA evidence for current gene models (for Arabidopsis thaliana, see the AtGDB site at http://www.plantgdb.org/AtGDB/).
    Keywords: Computational Biology ; Databases, Genetic ; Genes, Plant ; Genome, Plant
    E-ISSN: 1362-4962
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 4
    Language: English
    In: Genome biology, 2004, Vol.5(10), pp.R82
    Description: Derived from the maize Mu1 transposon, RescueMu provides strategies for maize gene discovery and mutant phenotypic analysis. 9.92 Mb of gene-enriched sequences next to RescueMu insertion sites were co-assembled with expressed sequence tags and analyzed. Multiple plasmid recoveries identified probable germinal insertions and screening of RescueMu plasmid libraries identified plants containing probable germinal insertions. Although frequently recovered parental insertions and insertion hotspots reduce the efficiency of gene discovery per plasmid, RescueMu targets a large variety of genes and produces knockout mutants.
    Keywords: Genome, Plant ; DNA Transposable Elements -- Genetics ; Mutagenesis, Insertional -- Genetics ; Zea Mays -- Genetics
    ISSN: 14656906
    E-ISSN: 1474-760X
    E-ISSN: 14656914
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  • 5
    Language: English
    In: Nucleic acids research, 01 July 2003, Vol.31(13), pp.3597-600
    Description: The GeneSeqer@PlantGDB Web server (http://www.plantgdb.org/cgi-bin/GeneSeqer.cgi) provides a gene structure prediction tool tailored for applications to plant genomic sequences. Predictions are based on spliced alignment with source-native ESTs and full-length cDNAs or non-native probes derived from putative homologous genes. The tool is illustrated with applications to refinement of current gene structure annotation and de novo annotation of draft genomic sequences. The service should facilitate expert annotation as a community effort by providing convenient access to all public plant sequences via the PlantGDB database, a simple four-step protocol for spliced alignment and visually appealing displays of the predicted gene structures in addition to detailed sequence alignments.
    Keywords: Genome, Plant ; Software ; Sequence Analysis, DNA -- Methods
    E-ISSN: 1362-4962
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  • 6
    Language: English
    In: Nucleic acids research, 01 January 2003, Vol.31(1), pp.244-7
    Description: Zea mays DataBase (ZmDB) seeks to provide a comprehensive view of maize (corn) genetics by linking genomic sequence data with gene expression analysis and phenotypes of mutant plants. ZmDB originated in 1999 as the Web portal for a large project of maize gene discovery, sequencing and phenotypic analysis using a transposon tagging strategy and expressed sequence tag (EST) sequencing. Recently, ZmDB has broadened its scope to include all public maize ESTs, genome survey sequences (GSSs), and protein sequences. More than 170 000 ESTs are currently clustered into approximately 20 000 contigs and about an equal number of apparent singlets. These clusters are continuously updated and annotated with respect to potential encoded protein products. More than 100 000 GSSs are similarly assembled and annotated by spliced alignment with EST and protein sequences. The ZmDB interface provides quick access to analytical tools for further sequence analysis. Every sequence record is linked to several display options and similarity search tools, including services for multiple sequence alignment, protein domain determination and spliced alignment. Furthermore, ZmDB provides web-based ordering of materials generated in the project, including ESTs, ordered collections of genomic sequences tagged with the RescueMu transposon and microarrays of amplified ESTs. ZmDB can be accessed at http://zmdb.iastate.edu/.
    Keywords: Databases, Genetic ; Genome, Plant ; Zea Mays -- Genetics
    E-ISSN: 1362-4962
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  • 7
    Language: English
    In: Plant Molecular Biology, 2011, Vol.77(3), pp.225-233
    Description: Allopolyploidization is considered an essential evolutionary process in plants that could trigger genomic shock in allopolyploid genome through activation of transcription of retrotransposons, which may be important in plant evolution. Two retrotransposon-based markers, inter-retrotransposon amplified polymorphism and retrotransposon-microsatellite amplified polymorphism and a microsatellite-based marker, inter simple sequence repeat were employed to investigate genomic changes in early generations of a newly synthesized allotetraploid Cucumis  ×  hytivus Chen & Kirkbride (2n = 4 x  = 38) which was derived from crossing between cultivated cucumber C. sativus L. (2n = 2 x  = 14) and its wild relative C. hystrix Chakr. (2n = 2 x  = 24). Extensive genomic changes were observed, most of which involved the loss of parental DNA fragments and gain of novel fragments in the allotetraploid. Among the 28 fragments examined, 24 were lost while four were novel, suggesting that DNA sequence elimination is a relatively frequent event during polyploidization in Cucumis . Interestingly, of the 24 lost fragments, 18 were of C. hystrix origin, four were C. sativus -specific, and the remaining two were shared by both species, implying that fragment loss may be correlated with haploid DNA content (genome size) of diploid parents. Most changes were observed in the first generation after polyploidization (S 1 ) and stably inherited in the subsequent three generations (S 2 –S 4 ), indicating that genomic changes might be a rapid driving force for the stabilization of allotetraploids. Sequence analysis of 11 of the 28 altered DNA fragments showed that genomic changes in the allotetraploid occurred in both coding and non-coding regions, which might suggest that retrotransposons inserted into genome randomly and had a genome-wide effect on the allotetraploid evolution. Fluorescence in situ hybridization (FISH) analysis revealed a unique distribution of retrotransposon and/or microsatellite flanking sequences in mitotic and meiotic chromosomes, where the preferential FISH signals occurred in the centromeric and telomeric regions, implying that these regions were the possible hotspots for genomic changes.
    Keywords: Polyploidization ; Evolution ; Retrotransposon ; Cucumis ; IRAP ; REMAP ; Fluorescence in situ hybridization (FISH)
    ISSN: 0167-4412
    E-ISSN: 1573-5028
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