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Database Commons - PIECE

PIECE

Citations: 27

z-index 2.11

Short name PIECE
Full name Plant Intron Exon Comparison and Evolution database
Description IECE is a plant gene structure comparison and evolution database with 25 species. Annotated genes were extracted from the species and classified based on Pfam motif. Phylogenetic tree was reconstructed for each gene category integrated exon-intron and protein motif information. Both the sequences and gene structure information for each identified gene are freely available for online access on the PIECE website.
URL http://wheat.pw.usda.gov/piece/
Year founded 2012
Last update & version 2017-01-01    v 2.0
Availability Free to all users
University/Institution hosted United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Western Regional Research Center
Address Crop Improvement and Genetics Research Unit
City Albany
Province/State California
Country/Region United States
Contact name Yi Wang
Contact email yi.wang@ars.usda.gov
Data type(s)
Major organism(s)
Keyword(s)
  • gene structure
  • Phylogenetic tree
Publication(s)
  • PIECE 2.0: an update for the plant gene structure comparison and evolution database. [PMID: 27742820]

    Yi Wang, Ling Xu, Roger Thilmony, Frank M You, Yong Q Gu, Devin Coleman-Derr
    Nucleic acids research 2017:45(D1)
    0 Citations (Google Scholar as of 2017-02-20)

    Abstract: PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron-exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 (http://probes.pw.usda.gov/piece or http://aegilops.wheat.ucdavis.edu/piece). PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version. In the current version, we also added several new features: (i) a new viewer was developed to show phylogenetic trees displayed along with the structure of individual genes; (ii) genes in the phylogenetic tree can now be also grouped according to KOG (The annotation of Eukaryotic Orthologous Groups) and KO (KEGG Orthology) in addition to Pfam domains; (iii) information on intronless genes are now included in the database; (iv) a statistical summary of global gene structure information for each species and its comparison with other species was added; and (v) an improved GSDraw tool was implemented in the web server to enhance the analysis and display of gene structure. The updated PIECE 2.0 database will be a valuable resource for the plant research community for the study of gene structure and evolution. © Crown copyright 2016.

  • PIECE: a database for plant gene structure comparison and evolution. [PMID: 23180792]

    Yi Wang, Frank M You, Gerard R Lazo, Ming-Cheng Luo, Roger Thilmony, Sean Gordon, Shahryar F Kianian, Yong Q Gu
    Nucleic acids research 2013:41(Database issue)
    27 Citations (Google Scholar as of 2017-02-20)

    Abstract: Gene families often show degrees of differences in terms of exon-intron structures depending on their distinct evolutionary histories. Comparative analysis of gene structures is important for understanding their evolutionary and functional relationships within plant species. Here, we present a comparative genomics database named PIECE (http://wheat.pw.usda.gov/piece) for Plant Intron and Exon Comparison and Evolution studies. The database contains all the annotated genes extracted from 25 sequenced plant genomes. These genes were classified based on Pfam motifs. Phylogenetic trees were pre-constructed for each gene category. PIECE provides a user-friendly interface for different types of searches and a graphical viewer for displaying a gene structure pattern diagram linked to the resulting bootstrapped dendrogram for each gene family. The gene structure evolution of orthologous gene groups was determined using the GLOOME, Exalign and GECA software programs that can be accessed within the database. PIECE also provides a web server version of the software, GSDraw, for drawing schematic diagrams of gene structures. PIECE is a powerful tool for comparing gene sequences and provides valuable insights into the evolution of gene structure in plant genomes.

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Tags

DNA
Plant
gene structure Phylogenetic tree

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Shixiang Sun [2017-02-20]
    • Shixiang Sun [2016-03-25]
    • Shixiang Sun [2015-11-21]
    • Shixiang Sun [2015-06-28]
    • Shixiang Sun [2015-06-26]
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