Welcome to MaizeSequence.org

This site provides sequence and annotation of the Zea mays ssp. mays genome resulting from the Maize Genome Sequencing Project. The browser is based on the July 2005 release of the AGI Agarose FPC Map and on BAC clone sequences contained therein.

Sequencing of the B73 cultivar commenced in November 2005 as part of a 3-year multi-institutional collaboration funded jointly by the NSF, USDA, and DOE. The strategy is to individually sequence a set BAC clones across a minimal-tiling path. Gene space will be identified and sequenced to finished quality. Read more about the Maize Genome Project or view the current sequencing progress.

Our goal is to provide full and up-to-date access to all sequenced maize data. In addition to the latest sequenced BAC clones, the site presents preliminary annotations that are computationally derived from the sequence data. Annotations include predicted genes, markers, repeats, and expressed and conserved regions.

The site presents convenient entry points into the maize genome:

  • Browse the genome visually through the EnsEMBL genome browser [More Information].
  • Search for specific maize data through a unified feature name search (top-right-hand corner) or through our BLAST server.
  • Download entire data sets via FTP.
  • Get notified when new data arrives through our RSS notification system.

News

February, 2008

  • Press Release: Researchers Map Corn Plant's Genome
  • Evidence-based gene builds are available alongside ab initio gene predictions
  • Whole-genome alignment between maize BACs and the Rice (Oryza sativa ssp. japonica) has been conducted and sequence-based synteny tracks are now available on BAC sequence maps
  • The raw maize databases are now available on the FTP site as downloadable archives

January, 2008

  • Maize sequences and annotations have been updated to include the latest sequences available in Genbank.
  • The website now features a new look-and-feel. We hope you like it!
  • Raw Phred quality scores are now available for individual BACs (ContigView). Quality scores are visualized as continuous score plots and can also be exported as raw Phred values.
  • Hybridized markers on FPC map views (CytoView) are now consolidated into one track. Each marker set is distinguished by color.
  • Sequence-based features are now projected on FPC map views. These features include predicted genes, aligned data markers (ESTs, GSSs, FSTs, and arrays), as well as repeat annotations.
  • A Genes menu on ContigView now controls display of classes of gene predictions (i.e. Hypothetical, Transposon-like, Protein-coding).

August, 2007

  • Download entire data sets through our new FTP server
  • Subscribe to a customizable RSS feed of a specific region of interest.
  • BLAST specific data sets, such as HTGS_IMPROVED bacs, BAC-end sequences, or predicted gene translations
  • Access earlier versions of BAC clones to monitor how a clone and its underlying annotations have evolved over time.

As always, we would like to get your feedback about both new and existing features to the site.