Protein Alignment Table for Zea mays

What type of data does the Protein Alignment Table display?

The Maize Genome Sequencing Project currently deposits maize BACs to GenBank at a rate of several per day. Our annotation workflow retrieves these BACs every night and provides tentative annotation views based on transcript evidence and mapping of putative rice and sorghum proteins. This table displays protein alignments (splice-aligned by GenomeThreader) from this pipeline, including their aligned position and functional annotations. NOTE: Because most of the deposited BACs are unfinished (Phase 1), some of the predicted gene models may be incomplete and their order may be not be correct.

How can I use the Protein Alignment Table?

The table below organizes the ZmGDB annotation results by date, BAC, and alignment position. The most recently annotated BACS are first. If you have a favorite gene with similarity to a rice or sorghum gene, you can find all BAC locations where it aligns with high similarity. All alignments are ordered along each BAC, so you can also scan for other genes of interest nearby and identify regions of colinearity between maize and the model species. You can also create on-the-fly multigenome aligments using direct links to CoGe (details). In addition, Ds insertions from the AcDs Tagging program are cataloged in this table and can be searched or selected ("Show only fDs BACs"). Retrotransposons and transposons are filtered out by default (by keyword and frequency) but can be viewed if desired ("Show Retrotransposons").

Table Tips:

• To search for an aligned protein by ID or description, use the search box or click on one of the IDs or descriptions in the table
• To search for a specific BAC, contig, or chromosome, use the search box or click on one of the IDs or descriptions in the table
• To view the region in genome context, click the icon in column 1.
• To view a multigenome comparison of the region to sorghum or rice, click the CoGe icon in column 2 (links to GEvo Genome Evolution Analysis tool).
• For quick table tips, hover over any underlined link.

Need more information?

For additional details go to our ZmGDB Help Pages.