QUERIES
If you have suggestions toward adding additional queries, or styles of queries, to make your life easier
I recommend adding your comments to the NSF Wheat Project Bulletin Board.
All suggestions will be used to build desired queries and listed here. You may even be able to construct one
yourself using the tools provided below, but if you don't know how, it is our pleasure to do it for you.
These are tables constructed from the ACEDB wEST database. The benefits of these tables are speed in display
and various filtering options.
Mapped Loci -
This is a form for querying tentative mapped loci for ESTs used as deletion mapping probes.
Results can be filtered in various ways.
EST BLAST Results -
This is a special form for querying nucleic acid (BLASTN) or peptide (BLASTX) match descriptions for sequences in the
wEST database. ESTs were BLASTed against the NCBI Genbank non-redundant databases.
TABLEMAKER QUERIES
The ACEDB Tablemaker program queries the wEST database directly using the webace2 package, instead of the usual
AceBrowser web display. The requests for Locus information are fairly quick (because there are relatively
few entries at this time); however, a Tablemaker or Simple Query within the Sequence class can be quite
computer resource intensive (we have over 80,000 ESTs and pointers to over 500,000 sequence annotations).
It is recommended to use the MySQL tables (shown above) instead to save time on Sequence class queries.
If you attempt a computer intensive request through the web it will probably time-out and you would have
spent your 10 minutes waiting for the results for nothing,
so beware.
Because there are over 50,000 entries, the query will sometimes time-out. A previous tracefile list has been
created and is available as a file called GGtracelist.txt (5923348 bytes).
The paths listed are derived from the current tracefile server (opal.pw.usda.gov).
This will list a collection of tracefiles available as listed in the GrainGenes database:
Sequence Other_name Library Tracefile_Path
In this collection of Queries to the wEST database, you will see Mapped Loci positioned in columns as:
Locus Chr Arm Bin Size_Kb Accn Image
In this collection, candidate genes (based on the best nucleic acid match in the non-redundant database) are
listed with locus.
These are Loci which were not resolvable by the hybridization data to the deletion line series tested.
Locus Unmapped_Chr_Class Probe Deletion_Line_Scored Image_Link Remarks
The second query is the same as the first except results are restricted only to loci with special remarks which may guide bin assignment.
The loci entries containing the standard remark "band x of y for probe z" has been removed.
This excludes unmapped loci for which no band was scored in the deletion series (the same pattern would be detected in the entire series, or part
of the series would be missing in the hybridization tests).
Below is the older query without the Image links
Locus Unmapped_Chr_Class Probe Deletion_Line_Scored Remarks
The second query is the same as the first except results are restricted only to loci with special remarks which may guide bin assignment.
The loci entries containing the standard remark "band x of y for probe z" has been removed.
Mapped Loci with Candidate IDs (same pattern as above collection, except with Candidate added)
In this collection, candidate genes (based on the best nucleic acid match in the non-redundant database) are listed too, in this format:
Locus Chr Arm Bin Size_Kb Candidate