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:

1a.49 June 2008

Freeze Version: 1
Release Date	June 2, 2008
Freeze Date	March 21, 2008
Total BACs	15,521
Total DNA	2,580,594,598 bp
Annotation Build: a
Fgenesh Predictions Peptide Classification Protein Annotations Whole-Genome Alignments (Rice) Repeat Masking (MIPS) Electronic SSRs Cereal Alignments
Ensembl Version: 49

Sequence Statistics

	FULLTOP	PREFIN	ACTIVEFIN	IMPROVED	Total
Clones	686	3,985	4,439	6,409	15,521
Nucleotides	96.1 Mb	676.7 Mb	724.3 Mb	1,074.1 Mb	2,580.6 Mb
Contigs	12,668	40,950	48,678	67,257	170,243
Average per Clone	18.5	10.3	11.0	10.5	10.9
Minimum per Clone	1	1	1	1	1
Maximum per Clone	40	38	37	60	60

Ab initio Gene Statistics

Gene Classification	Count	Ratio	Average Transcript Length	Median Transcript Length	Density (Genes per Mb)
Protein-Coding	73,042	15.25%	1,251 bp	936 bp	28.1
Hypothetical	83,814	17.50%	476 bp	383 bp	32.3
Transposon-like	322,092	67.25%	1,779 bp	1,442 bp	124.1
Total	478,948	100.00%	1,686 bp	1,251 bp	184.5

Repeat Statistics

MIPS/REcat Repeat Type	Nucleotides	Coverage Ratio
All Repeats	2,083.0 Mb	80.23%
Class I Retroelements	2,010.5 Mb	77.43%
Class II/III Transposable Elements	50.4 Mb	1.94%
Other	22.1 Mb	0.85%
Non-Repeat	513.4 Mb	19.77%

News

New release 1a.49 (June, 2008)
We have migrated to a new versioning scheme that encodes the sequence data freeze, the computed annotation build, and a software revision. The new release (1a.49) of the maize genome includes 15,521 annotated maize BAC clones.
Sequence-based electronic SSRs
Putative electronic SSRs (Short Sequence Repeats) have been mined on individual BAC sequences. A new track on ContigView is included, and the "Repeat Features" track on CytoView now provides SSR counts
MDR density plots
The MDR (mathematically-defined repeats) track on ContigView has been replaced by a continuous density plot. The raw data is available for download as quantitative FASTA dumps.
Improved Site News
News are now database-driven, allowing us to provide more frequent news updates and to keep users notified. You can subscribe to our news RSS feed.
Whole-genome alignments
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.
Evidence-based Genes
Evidence-based gene builds are available alongside ab initio gene predictions.
Release of the maize draft sequence
An announcement was released to the press that a draft of the maize genome sequence is now available. The draft release represents complete coverage of the genome. Over the course of 2008 the quality of the sequence will be improved.
MySQL Database dumps
The raw maize databases are now available on the FTP site as downloadable archives
Sequence and annotation dumps
Download entire data sets through our new FTP server
New look-and-feel
The website now features a new look-and-feel. We hope you like it!

Release History

Freeze Version: 0.9
Release Version	0.9a.48
Release Date	February 27, 2008
Freeze Date	December 11, 2007
Total BACs	14,423
Total BAC contigs	196,799
Contigs per BAC	13.6
Total DNA	2,314,656,711 bp
Annotation Build: a
Evidence-based Genes	62,913
Fgenesh Models	420,732
Protein-coding Genes	64,837
Hypothetical Genes	72,109
Transposon-like Genes	283,786
Fgenesh Predictions Peptide Classification Protein Annotations Whole-Genome Alignments (Rice) Repeat Masking (MIPS) Electronic SSRs Cereal Alignments
Ensembl Version: 48

Roadmap

The following is a tentative release schedule for MaizeSequence.org:

1b.49 (June 2008)
- Data Freeze 1 (15,521 BACs)
- Evidence-based genes
2a.49 (July 2008)
- Data Freeze 2 (approximately 16,500 BACs)
- FGENESH predictions
- Cereal alignments
- Repeat analysis
2b.50 (August 2008)
- Data Freeze 2 (approximately 16,500 BACs)
- Evidence-based genes
- functional annotations