How to use DAIZUbase: A unified soybean genome database

Version0.2 13/May/2009

Outline
1. System overview
2. Top page
3. Browsers and viewer
3.1UnifiedMap
3.2 GBrowse
3.3 GeneViewer
4. Word search and sequence search
4.1 An example of keyword search
4.2 An example of sequence search11. System overview
DAIZUbase is a unified soybean genome database with 2 map browsers and 1 gene viewer.
* UnifiedMap : physical map and genetic linkage map with BAC contig, and BAC-ends for each chromosome.
* GBrowse : genome annotation viewer based on GBrowse developed by GMOD.
* GeneViewer : gene information viewer based on the gene viewer of RiceGAAS/KAIKOGAAS.
Top PageSearch ResultSearch

GBrowseUnifiedMap

GeneViewer22. Top pageThe top page provides access to soybean genome (Williams82, ENREI) information.
1) Keyword Search: Input a keyword and choose from “Search Field”, “Search Chromosome”, and “Search Data Set” to delimit the search.
The data sets include genes, FLcDNAs, markers, BAC ends, and BAC clones.
2) Sequence Search: Using the BLAST system with Glycine max (Williams82) and ENREI BACend sequence as a reference
database. Nucleotide or amino acid sequence can be used as query. Upon clicking the “BLAST” link, a query input page is opened.

Keyword SearchSequence Search (BLAST)A query input page3

3. Browsers and viewer
3.1 UnifiedMap
3.2 GBrowse
3.3 GeneViewer

43.1 UnifiedMap[Objective]- linkage map and physical map showing Williams82 scaffolds, BAC contigs, BAC ends, and markers for each chromosome.
[Link]- Choose designated region on the physical map and link to GBrowse or get to sequence.
- Choose designated region on the linkage map. A red arrow appears on right side if marker information is available.
1. Select a chromosome
2. Specify the zooming level.
3. Check the desired items for display.2
Specify the region in thelinkage map by moving
the red frame.
Detailed
information isshown upon
pointing thecursor.
Specify theregion in thephysical map
by moving theblue frame.

53.2 GBrowse[Objective]- Genome annotation viewer with a graphical representation of a section of a genome.

GBrowse_details[Link]- Click designated region on Details and sequence and ID are displayed in another page.
- Click gene model on Details for link to GeneViewer.
Click a location to viewon Overview, display
location is changed.

GeneViewer

Check display items so display items are changed.

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3.3 GeneViewer[Objective]- Gene information viewer, showing the detailed information of the gene model.
[Link]- “Search Results” links to results of homology search using BLASTn, BLASTp, HMMER and ProfileScan with corresponding alignmentsof the sequence.
- “Analysis of amino acid sequences” links to PSORT, SOSUI, MOTIF and Gene ontology (InterProScan).
- “Sequence” links to the nucleotide sequence, spliced nucleotide sequence and translated protein sequence of the predicted gene.

Result of domain search against Pfam database.

Detailed information of the predicted gene including chromosome number,clone name, position of exons and GC content.

Results of homology search using BLASTn (top 3 ESTs),
BLASTp (top 10 proteins), HMMER and ProfileScan with the correspondingalignments of the sequence.

Display the results of queries to amino acid analysis server/site
such as PSORT, SOSUI,MOTIF and Gene ontology (InterProScan).
Links to the nucleotide sequence, spliced nucleotide sequence andtranslated protein sequence of the predicted gene.

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4. Keyword search and sequence search
4.1 An example of keyword search
4.2 An example of sequence search

84.1 An example of keyword search

Search for “00230” ingene data set onchromosome 5.

Enter “00230” in query box
Choose ID from pull-down menu
Choose “Gm5”
Click “Glyma1 annotation”
Click “Search” button.

Result of keyword search

94.2 An example of sequence search
Search for locationof a nucleotide
sequence onWilliams82.
This URL allows the user
to redisplay the result offor a certain period.

Choose Blastn
and Williams82

Uploadquery sequence file
Result of sequence search
Set parameters

Click “Search” button

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