Release Version

Versioning Scheme

The release version is composed of 3 components in the form Nx.E:

N: An integer representing the data freeze version
x: A lowercase letter indicating the annotation build that was performed on the data freeze
E: An integer indicating the major Ensembl code revision

Together, the release version refers to a particular set of maize clones along with their annotations. The annotation build represents a set of computational analyses that have been performed on the specific sequence freeze.

We will likely provide incremental release updates as new annotations become available for the same data. In that case, only the lowercase letter will be incremented (e.g. 1a.49 → 1b.49).

Release Version

The current release version of the MaizeSequence.org portal is:

3b.50 February 2009

Freeze Version: 3
Release Date	February 24, 2008
Freeze Date	October 31, 2008
Total BACs	16,587
Total DNA	2,778,853,373 bp
Annotation Build: b
Filtered Gene Set Evidence-based Genes (Gramene GeneBuilder) Fgenesh Predictions Working Gene Set Peptide Classification Protein Annotations Functional Annotations Whole-Genome Alignments (Rice) Repeat Masking (MIPS) Electronic SSRs Cereal Alignments
Ensembl Version: 50

Sequence Statistics

	FULLTOP	PREFIN	ACTIVEFIN	IMPROVED	Total
Clones	424	113	2,032	14,018	16,587
Nucleotides	59.1 Mb	16.7 Mb	335.6 Mb	2,367.5 Mb	2,778.9 Mb
Contigs	7,260	1,105	22,627	154,240	185,232
Average per Clone	17.1	9.8	11.1	11.0	11.2
Minimum per Clone	1	2	1	1	1
Maximum per Clone	40	30	37	64	64
Average Contig Length	8,137 bp	15,071 bp	14,832 bp	15,350 bp	15,002 bp
Minimum Contig Length	1,026 bp	1,182 bp	325 bp	2 bp	2 bp
Maximum Contig Length	114,702 bp	107,879 bp	173,121 bp	216,833 bp	216,833 bp

Gene Statistics

Gene Type	Genes	Transcripts	Average Transcript Length	Median Transcript Length	Density (Genes per Mb)	Transcripts per Gene
Evidence-based Genes	90,829	125,435	3,598 bp	2,512 bp	32.7	1.38
Working Gene Set	113,672	148,280	2,690 bp	1,643 bp	40.9	1.30

News

Download the Filtered Gene Set
The Filtered Gene Set (FGS) is now available on our FTP site. We are still working hard to release the new site with the chromosome assemblies as part of the browser, but in the meantime we wanted to share a definitive set of genes that were annotated and validated by cross-species analysis.
Delay of Release 4a.53
Release 4a.53 is being delayed and will be made available at the end of June, instead of April 29, 2009. We apologize for any inconvenience that this may cause. Read more about the delay as well as our intentions for the release here.
Download the maize golden path
The maize golden path (AGP v1) can be accessed in FASTA and AGP formats from the Arizona Genomics Institute.
Intentions for Release 4a.53
Release 4a.53 is expected on ~~April 29, 2009~~ May 27, 2009. The release will include, among others, a maize genome golden path, an improved working gene set, and a new version of the browser. Read more about our intentions for the release here.
Tour the Project!
Experience an interactive demo covering many aspects of the sequencing project.
Release 3b.50 (February, 2009)
An incremental annotation-based release that includes a new filtered gene set and several website enhancements
Filtered Gene Set
A subset of the Working Gene Set that has been filtered to remove pseudogene, TE-encoded genes, and partial models
Updated FTP dumps
The FTP site has been reorganized to provide different data sets in a variety of formats. All gene sequence dumps now include CDS sequences as well.
We're now on Twitter!
You can keep up with the latest news and bulletins by following us on Twitter, or read updates from the left navigation bar.
Reorganized menus
Menus on the BAC-based genome browser have been simplified and standardized with the Gramene genome browser.

Older News

Release 2a.50 (October, 2008)
The current release of the maize sequence features DNA and annotation of 16,205 BACs, including over 4,000 BAC updates. An evidence-based gene build is presently in progress and should be available at the end of October. For more information, please refer to the release page.
Functional annotations now available
Functional annotations, including Gene Ontology (GO) and other descriptions of specific genes, are now computed by the Xref system
Release 3a.50 (December, 2008)
This release of the maize sequence includes DNA and annotation of 16,587 BAC clones. It includes close to 3 billion bases of maize sequence. Over the course of 2009 we will continue to work on gap-filling sequences and to provide important annotation builds and data updates. For example, in the next 3 months we expect to release, in close collaboration with Gramene, fully-annotated phylogenetic trees describing evolutionary relationships among maize, rice, and sorghum gene orthologues. You can find more information about the current release as well as a short-term website roadmap on our release page.
The Working Gene Set
Release 3a.50 features a set of non-overlapping genes that cover the entire maize genome. The set consists of over 90,000 evidence-based genes computed by the Gramene GeneBuilder, complemented by a set of more than 20,000 ab initio Fgenesh predictions that were computed on RepeatMasked sequence whose loci are not covered by the evidence-based set
BLAST server improvements
We have made several performance-related and visual enhancements to BlastView. These improvements should restore stability of the BLAST functionality

Release History

BAC Freeze
Release Version	3b.50	3a.50	2a.50	1a.49	0.9a.48
Release Date	February 24, 2009	December 8, 2008	October 14, 2008	June 2, 2008	February 27, 2008
Freeze Date	October 31, 2008	October 31, 2008	June 21, 2008	March 21, 2008	December 11, 2007
Total BACs	16,587	16,587	16,205	15,521	14,423
Total BAC contigs	185,232	185,232	175,964	170,243	196,799
Contigs per BAC	11.2	11.2	10.9	10.9	13.6
Total DNA	2,778,853,373 bp	2,778,853,373 bp	2,694,963,615 bp	2,580,594,598 bp	2,314,656,711 bp
Annotation Build
Evidence-based Genes	90,829	90,829	62,696	62,913	62,913
Fgenesh Models	81,453^*	514,467	498,710	478,948	420,732
Protein-coding Genes	54,606	59,052	57,480	73,042	64,837
Hypothetical Genes	18,352	86,201	83,359	83,814	72,109
Transposon-like Genes	8,495	369,214	357,871	322,092	283,786
Analyses
Fgenesh Predictions	×^*	×	×	×	×
Gramene GeneBuilder	×	×		×	×
Peptide Classification	×	×	×	×	×
Protein Annotations	×	×	×	×	×
Whole-Genome Alignments (Rice)	×	×	×	×	×
Repeat Masking (MIPS)	×	×	×	×	×
Electronic SSRs	×	×	×	×	×
Cereal Alignments	×	×	×	×	×

^* — As of Release 3b.50, Fgenesh ab initio gene models are computed on repeat-masked sequence. In previous releases, ab initio gene models were computed on raw sequence and transposon-like predictions were then classified. We believe that the new strategy yields higher-confidence ab initio gene models.

Roadmap

The following is a tentative release schedule for MaizeSequence.org. Because of the dynamic nature of the sequencing project, the delivered data sets and features may change. We do, however, strive to keep the roadmap up-to-date. Follow us on Twitter or subscribe to our RSS feed to stay informed.