ZmDB, an integrated database for maize genome research.

Qunfeng Dong; Laura Roy; Michael Freeling; Virginia Walbot; Volker Brendel

doi:10.1093/nar/gkg082

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ZmDB, an integrated database for maize genome research.

Qunfeng Dong·Laura Roy·Michael Freeling·Virginia Walbot·Volker Brendel

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Abstract

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/.

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DNA Transposable Elements Databases, Genetic Expressed Sequence Tags Gene Expression Genome, Plant Mutation Oligonucleotide Array Sequence Analysis Phenotype Plant Proteins Zea mays Journal Article Research Support, U.S. Gov't, Non-P.H.S.

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Qunfeng Dong, Laura Roy, Michael Freeling, Virginia Walbot, Volker Brendel. 2003-01-01. ZmDB, an integrated database for maize genome research.. https://doi.org/10.1093/nar%2Fgkg082

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