Alignments to Genome
Spliced-alignments include
EST,
cDNA,
PUT,
Os-PEP,
Probe; DNA alignments include
none.
More about alignments...
Aligned Sequence Types and Totals at ZmGDB. TBD.
Search/Download
Revtrieve any combination of splice-aligned sequences, gene models, or genomic sequence (including 5' or 3' flanking sequence), from ZmGDB.
More about search / download...
| Resource |
Description |
| Search by ID / Keyword |
Search for any ZmGDBgene or aligned sequence by ID or keyword, and download complete sequence or flanking 5' or 3' regions, exons, or introns (FASTA format).
|
| Download Region Data |
For any specified genomic region, download genomic DNA (FASTA format), all aligned/computed transcripts or proteins (FASTA format), or all genome annotations (GenBank, GFF3 or EMBL format).
|
| Download All |
Download bzip2 files and MySQL tables representing complete ZmGDB dataset |
View the latest Zea mays sequence count at PlantGDB
Tools
Sequence analysis tools accessed from the Genome Context View menu will use the current genomic region as input. Or, to access the same tools without a genomic context, use ZmGDB left menubar Tools links.
and
GeneSeqer.
More about tools...
Online Analytical Tools - Description
| Name |
Description |
Source/Version |
| BLAST |
Use BLASTn, BLASTp, tBLASTn and tBLASTx to match a query sequence to ZmGDB sequences.
BLAST-able datasets include Zea mays genomic DNA, splice-aligned transcripts and proteins, gene models, and other aligned sequences. |
NCBI Blastall 2.2.18 |
| GeneSeqer |
Spliced alignment of user-specified transcript datasets to genomic DNA from any region in ZmGDB. User can specify splice site model and stringency level. |
Brendel Group (Oct 2008) |
| GenomeThreader |
Spliced alignment of user-specified protein datasets to genomic DNA from any region in ZmGDB. User can specify splice site model and stringency level. |
GenomeThreader Home Page |
Community Annotation
Community-contributed gene models for ZmGDB (
see Overview), generated using the yrGATE annotation tool, aided by
GAEVAL tables that flag problematic gene models.
Custom Track Display
Distributed Annotation Service (DAS) (
see Overview) is available for displaying remotely served genome alignments at ZmGDB, as well as for displaying selected ZmGDB tracks on a different genome browser (e.g. Ensembl, GBrowse).
How to use DAS...
To add a DAS track to ZmGDB using our DAS client, first select desired genome coordinates above and click "Go", then select menu item "Configure -> Add Track" and paste in the appropriate DAS URL.
To view ZmGDB tracks in another genome browser (e.g. Ensembl, Gbrowse) using our DAS server, first find the appropriate xDAS Server URL on our DAS overview page, then follow instructions on the remote browser website for adding the remote track. NOTE: DAS service available for certain tracks only.
For more details, refer to DAS section in our Genome Browser help pages.
Additional custom track display features are under development.
Annotated protein alignments
Annotated Protein Alignments: A
searchable table of splice-aligned, annotated protein models. TBD.
Support
Help pages and tutorials focussing on genome browser features and gene annotation. See side bar.