MaizeSequence Help

Please refer to the GeneBuilder help page for a full treatment on the Gramene gene-building process.

The Working Gene Set provides an overall representation of non-overlapping candidate gene elements across the maize genome sequence. It is constructed by complementing evidence-based genes predicted by GeneBuilder with ab initio gene models predicted by Fgenesh on RepeatMasked sequence. Only Fgenesh models that do not overlap with the evidence-based genes are used in the set.

The Filtered Gene Set is a subset of the Working Gene Set that was produced after several selection criteria were applied. These included screening out transposable element sequences, pseudogenes, and annotations whose coding sequence was < 150 nt. Additional considerations included homology to other genome annotations and evidence based on maize full-length cDNA clones.

Both sets are provided as individual gene tracks on the genome browser, and can also be downloaded en masse through the FTP site

Yes. We were able to retain 44,083 of the 113,670 genes from Release 3b.50 (38.782%) in Release 4a.53. These are all evidence-based genes whose structure had not changed at all by projection to the chromosome or by new evidence and GeneBuilder protocol [More info].

There could be any number of reasons why you can't find your sequence. If it's a clone contig or segment, that clone could have been either (a) replaced with a newer version, or (b) subsumed in the genome assembly (its sequence was unused, probably because of mutual overlap between its two flanking clones). If your sequence is a gene, it's quite possible that the gene was not retained in the new annotation build because the gene (a) could not be projected to the chromosome level (as a result of being anchored, say, to a subsumed segment), or (b) has a new genomic structure based on updated evidence or improved protocol.

In a 2005 paper, Ed Coe and Mary Schaeffer address these questions (page 299):

For the U.S. public genomic project, BAC libraries were initiated in 1998-1999. Three BAC libraries were constructed from the B73 inbred line, one of the two IBM mapping parents, for use in generating a physical map. The specific germplasm source for the B73 inbred line, PI 550473, is continuously and reliably available from the USDA North Central Regional PI Station at Ames, Iowa, and can be ordered through the Stock link at MaizeGDB.

Three different restriction enzymes were used to construct the libraries, to ensure comprehensive genome coverage. The HindIII library of 247,680 clones, ZMMBBb, constructed at Clemson University Genomics Institute (CUGI) (2005), has an average insert size of 137 kB and a genome coverage of ~17X. Characterizations showed this library to be representative and to be virtually free of chloroplast sequences (Tomkins et al, 2002). The HindIII library is available from the Arizona Genomics Institute (AGI) or from CUGI. An EcoRI BAC library, ZMMBBc (CHORI 201 segment 1), constructed at Children's Hospital Oakland Research Institute (CHORI), has an average insert size of 163 kB and a genome coverage of ~6.9X. An MboI library, ZMMBBc (CHORI 201 segment 2), constructed at CHORI in collaboration with Jo Messing, has an average insert size of 167 kB and a genome converage of ~7X. The EcoRI and MboI libraries are described by and can be ordered from CHORI. Hybridization filters for all three libraries are available from CUGI, AGI, and CHORI.

The paper provides further information about the BAC construction strategy. (made available with permission from Maydica)

Since the project aims to sequence the maize genespace, it is expected that regions on BACs that do not contain genes will not be sequenced to a finished quality. For more information, read about the various maize sequencing statuses.

In order to make better use of the space, all tracks are now configured via a separate Control Panel. The panel can be accessed by clicking on the "Configure this page" link on the left menu of all browser views. The Control Panel lets you add, remove, and configure which tracks are shown in the browser panels. The Control Panel also lets you manage your own user account, your bookmarks, and your private data.

Yes. The Ensembl browser supports DAS (Distributed Annotation System). Simply configure a URL to your custom data source (either through the Control Panel or from the sidebar) and a dedicated track should appear. We also provide a variety of pre-configured DAS tracks.

MaizeSequence.org is a replacement the maize browser on Gramene. Because the maize browser and the annotation pipeline are an integral part of the Maize Genome Sequencing Project and track its progress, data such as clones and underlying annotations is produced more rapidly. The browser therefore warrants its own website. Nevertheless, all cereal features between Gramene and MaizeSequence.org are deeply linked, and users should be able to navigate seamlessly between different genome maps provided by both browsers. Aside from an extensive set of enhancements, users should feel no different.

We strive to provide as much information on this site as possible. If a question does not appear in this FAQ, please use our feedback form to contact us. We will try our best to respond. If the question is general enough, and it usually is, we will post it on the FAQ.