Welcome to the Maize Microarray Annotation Database

This is a resource for obtaining annotations of the probes on the
Maize Agilent-016047 4x44k microarray.

Functionalities of the database:

1. Search Agilent Slide

Get the position of any probe(s) on the B73 genome sequence (v2)
as well as the functional annotation of its corresponding gene,
by submitting probe / gene / EST identifiers.

2. Blast sequences

Blast any sequence(s) against the Agilent slide to identify
which probes represent the query sequence best.

3. Get sequences from GenBank

Get DNA sequences from GenBank, by submitting any GenBank
accession numbers (only nucleotide databases are searched).

Please cite the Maize Microarray Annotation Database as follows:
Coetzer N, Myburg AA and Berger DK (2011) Maize microarray annotation database. Plant Methods 7 (1), 31 (http://www.plantmethods.com/content/7/1/31)

A global summary:

Probes were classified into six genomic annotation groups
Global bargraph
  1. Annotated by Sense Gene Model:
    Probes that match a Working Gene Set (WGS) transcript and genomic location of the same gene model
  2. Annotated by Antisense Gene Model:
    Probes that match the antisense direction of a WGS transcript and genomic location of the same gene model
  3. Annotated by gDNA:
    Probes that match a unique location on the maize B73 genome, but this location is not currently annotated as a gene model
  4. Annotated by EST:
    Probes that do not match a WGS transcript but that are derived from an EST that matches a WGS transcript, and its genomic location
  5. Ambiguous Annotation:
    Probes with more than one sense gene model, antisense gene model or EST result
  6. Inconclusive Annotation:
    Probes that match many transcripts, but not the genomic location of corresponding gene models

Please e-mail questions or comments to Nanette, or contact Nanette if you wish to download the database as a tab delimited text file.