Important for the first time user


We strongly recommend using Firefox to view our database. Please report any compatibility issues to the developer (see contact info).

The PIECE provide a cross-browser JavaScript viewer that draws gene structue and phylogenetic graphics. When accessing a gene family intron/exon page, if the family contains lots of members or intron/exon elements, your web browser accesses a very long javascript code, it will take time to process it. The browser prompts the user to decide whether they would like to continue running the script. For example:
Internet Explorer
timeout_ie

Firfox
timeout_firefox
If you want to complete the graphic, please let the browser continue running the script.

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About this database



What is PIECE?


PIECE is a Plant Intron Exon Comparison and Evolution database. It 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.

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Why is it different from existing databases?


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Usage


Browser compatibility


Although this website is designed for and therefore works the best on modern and cross-platform browsers like Firefox, Google Chrome and Opera, most of the functionalities work very well on most other web browsers. The following is an incomplete list: Currently it's known that some functions of the javascript viewer is shown differently under Microsoft IE6~8.

Please report any compatibility issues to the developer (see contact info).

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Search


The PIECE has a user-friendly entry point for searching each gene (Fig. 1).
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Fig. 1. The search system for the PIECE. (A) The user can select the search type and input the keywords. (B) select the plant species for the search. (C) Choose the number in each result page and whether show different gene models or not.

Users can retrieve any gene by a keyword search for gene ID, gene name, or gene function or by a BLAST search (Fig. 2) of the 933971 sequences (amino acid or nucleotide) of the 25 species.
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Fig. 2 Use BLAST tool to search gene in the PIECE.

The main page of the search result lists all genes meeting the searching criteria and gives some brief information, such as gene accession, gene description, source organism, gene annotation, Pfam domain and gene ortholog analysis link (Fig. 3).
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Fig. 3. The search result of the PIECE. (A) Clicking on a gene accession will display the details on the exon-intron information, including the genomic and transcript sequence. (B) Each gene in the search result contains the Pfam domain which was identified in its protein sequence. Clicking on a Pfam domain will show its phylogenetic tree with gene structure. (C) The ortholog analysis link will display the GLOOME and EXALIGN result of the gene.

Clicking on a gene accession will display the details on the exon-intron information, including the genomic and transcript sequence. Each gene in the search result contains the Pfam domain which was identified in its protein sequence. Clicking on a Pfam domain will show its phylogenetic tree with gene structure. The ortholog analysis link will display the GLOOME and EXALIGN result of the gene.

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Show gene structure with phylogenetic tree


The database provides a user-friendly graphical viewer that displays SVG-formatted output, which contains a gene structure and Pfam domain pattern diagram linked to a bootstrapped similarity dendrogram (Fig. 4).
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Fig. 4. The PIECE database viewer. Data of the LOX gene (PF00305) in Arabidopsis thaliana, rice, poplar and Chlamydomonas reinhardtii. (A) A dendrogram of sequences clustered according to the presence and similarity of extracted Pfam motifs. (B) A diagram that displays positional information of the gene structure in each sequence. (C) Operation panel for manipulating the output. Color pikcer and check boxes for display for intron, CDS, UTR, Pfam domain and intron phase, save button to save the output as PNG file. (D) Color for the plant species and search function to find ID in the phylogenetic tree.

Depending on the annotations present in the database, the veiewer is able to automatically recognize elements of the gene structure, such as coding exons, introns, UTRs and various types of labels. Default conventions are used to render exons (thick boxes), UTRs (thin boxes) and introns (thin boxes and grey color), but the user can modify shapes, dimensions and colors of each of the elements of the gene (Fig. 4). The viewer also contains various functions such as searching gene ID in the phylogenetic tree. When the ID is found in the tree, the ID will be highlighted with red color. In the viewer, the exon, intron and Pfam domain for each gene are showed, which users can freely select. The length of the exon, intron or domain will be displayed when user select it, and a sequence page link to each exon, intron or Pfam domain.

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Multiple type for gene structure display


The PIECE can map exon boundaries on genomic sequences, protein sequences or alignment protein sequences (Fig. 5).
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Fig. 5. Multiple type for display gene structure. (A) Genomic sequences (B) Genomic sequences aligned with Pfam motif (C) Protein sequences (D) Protein sequences aligned with Pfam motif (E) Multiple alignment protein sequences.

Usually, the basic components of a gene structure (UTRs, intron, exons) is displayed on genomic sequence. For finding relationships between exon/intron composition in the encoded proteins, exon boundaries are also mapped on protein sequence. As shown in Figure, the viewer in the PIECE database provides both amino acid–sequence-based and nucleotide-sequence-based exon/intron display for each Pfam domain. Users can select any protein domain of interest by clicking Pfam ID in the search result to make this display.

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Analysis gene structure evolution with ortholog group


The GLOOME and EXALIGN program can be executed for each orthologs group to display exon-intron gain, loss and conservation. In the PIECE, the output of GLOOME include plant species tree, gene structure display, intron site sequence logo and the expected number of events for each intron site. User can click the each box in the histogram, the viewer will show the intron site in the aligment protein sequence. The alignments were generated using Muscle, and the sequence alignment graphical display was implemented in Jalview. The GLOOME in the PIECE viewers provide useful analytical facilities for exploring the degree of conservation of intron evolution across proteins in the ortholog group and also for analyzing the distribution of exonic sequences within the aligned coding nucleotide sequences of domains.
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The EXALIGN viewer of PIECE can show the reconstruction of the evolutionary history of the structure of a family of orthologous genes. This viewer provides exon-intron display for orthologous genes from gene structure data sets linked to the dendrogram. The gene exon comparison between species is shown as colored lines. Different color means different exon comparison result. function5

In PIECE, each gene has a GECA link to view the orthologs that are aligned using their common introns detected by CIWOG. The similarities between orthologous sequences in the alignment are represented at the level of amino acids in the translated exons. A blue line links two amino acids if they are identical, a purple line indicates conservative substitutions, and intron type is detected by CIWOG.
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Datasets


Now, the PIECE contains genes identified in 25 plant species (see detail).

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Contact


The database is design and developed by Yi Wang. Please send comments and requests to Yi.Wang@ARS.USDA.GOV.

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