A: We have transformed the FPC bands to genomic coordinates using a conversion factor of 4900 bases per band. This number, however, should be treated as an approximation.

A: No. BAC clones are selected uniformly across the 550 FPC contigs. Seeds have been selected and clones are walked off of these seeds.

A: There are 3400 seed clones selected based on several criteria. They must:

• be identified by both the agarose and HICF FPC maps
• be associated with at least one overgo marker
• have at least one BAC end sequence
• be at least 800kb apart

More information is available at Arizona Genomics Institute's Maize FPC Map page.

A: 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.

A: Yes. The menu above the browser window lets you control which tracks are visible and which are not. Furthermore, the browser uses cookies to remember the decision for 2 months.

A: Yes. The Ensembl browser supports DAS (Distributed Annotation System). Simply configure a URL to your custom data source (either through a pull-down menu or from the sidebar) and a dedicated track should appear. We now provide pre-configured tracks for maize TwinScan transcripts produced by the Danforth Center.

A: Virtual bins are computational representations of genetic bins found on the maize genetic maps. We developed virtual bins by generating correspondences between the AGI FPC map and the IBM2 Neighbors map. Markers common to both maps on the same chromosome were then assigned chromosomal positions based on the AGI approximation of 4900 basepairs per fingerprint contig band and then clustered with respect to maize bin. For any given bin, those markers outside of three deviations from the mean were discounted as spurious. Virtual bin boundaries were automatically calculated from the remaining minimum and maximum positions of markers in a cluster. Following automatic generation, we manually curated bin positions to assure no overlaps.

A: Mathematically defined repeat (MDR) tracks indicate regions of repetitive DNA. The frequency of each constituent 20-mer along the BAC sequence was determined within the raw reads of the maize whole genome shotgun sequence (DOE Joint Genome Institute). The numeric portion of the track name indicates the minimum frequency required for a region to be highlighted. Thus, highlighting in the "MDR repeats=2" track indicates regions over which 20-mers occurred two or more times; The "MDR repeats=10" indicates regions over which 20-mers occurred ten or more times; "MDR repeats=100", one hundred or more times; and "MDR repeats=1000", one thousand or more times. The most repetitive regions correspond to highlighted regions in the MDR repeat=1000 track. The least repetitive regions correspond to non-highlighted areas in the MDR repeat=2 track.

A: Predicted peptides are screened to distinguish those encoded by transposable elements (TE). Sequences are aligned to the NCBI non-redundant protein database using BLASTP. Those that align to transposable element sequences, as specified within a curated database, are classified as TE and are color-coded maroon within the browser's ContigView. Those not classified as TE are color-coded blue. FGENESH can predict coding sequences that incorrectly contain components of two genes. Approximately 3% of genes classified as TE are "fusions" that contain portions of non-TE genes.

A: Prediction translations are run through NCBI BLASTP using the default parameters. By default, the BLAST low-complexity filter is on. The website, on the other hand, turns off the filter by default, showing alignments which are considered unreliable for our classification purposes.

A: The improved clone sequences furnished by the browser are a direct representation of GenBank accession records. As such, the coordinates of the sequences and their underlying features have not been altered in any way. The highly-repetitive nature of the sequences makes it difficult to elucidate further contig order and orientation at this time.

We have gone to great lengths to ensure consistency and to prevent any incongruence between the data available at NCBI and the data we provide. We hope to make our approach to analyzing the emerging maize genome sequence as transparent as possible.

A: Sequenced BAC updates are provided on a weekly basis (Mondays). We regularly download BAC sequences, run them through our automated annotation pipeline, and validate the quality of analysis. All data produced by our pipelines can be easily exported. Most other data sets, such as reference feature maps, will remain relatively unchanged. We intend in the future to assess and enrich the maize FPC map by integrating sequence-based annotations.

A: 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.

A: 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.