MaizeSequence.org FTP Site
==========================

This site provides access to the latest sequenced maize data. The site is part
of the NSF-funded Maize Genome Sequencing Project.

The directories are named using the 'YYYYMMDD' date format, and their content
includes sequence data as of the indicated date. The 'current' directory
points to the most current data directory.

+----------------------------------------------+
| Release 1a.49                                |
+--------------------------+-------------------+
| Freeze Date              |    March 21, 2008 |
| Maize BAC clones         |            15,521 |
| Maize BAC contigs        |           170,243 |
| Contigs per BAC          |              10.9 |
| Sequence Length          |  2,580,594,598 bp |
+--------------------------+-------------------+
| Evidence-based Genes     |            62,913 |
| Fgenesh Models           |           478,948 |
|    Protein-coding Genes  |            73,042 |
|    Hypothetical Genes    |            83,814 |
|    Transposon-like Genes |           322,092 |
+--------------------------+-------------------+

Files
-----

Each directory contains the following files:

BACS.fasta           - Raw maize genome sequences for accessioned BACs, as
                       stored in GenBank
BACS_rm.fasta	     - RepeatMasked maize genome sequences for
                       accessioned BACs	     
BAC_contigs.fasta    - Sequences for all individual contigs that make up the
                       accessioned BACs
BAC_contigs_rm.fasta - RepeatMasked sequences for individual BAC-contigs
fpc_report.txt       - A table describing which clones on the agarose FPC
                       map have been accessioned (sequence present)
evidence-genes_fpc-mappings.txt
		     - A table showing the FPC location/annotation of BACs
		       on which evidence-based genes were called
protein-coding_fpc-mappings.txt
		     - A table showing the FPC location/annotation of BACs
		       on which protein-coding genes were called
TE-LIKE_GENES.fasta  - Nucleotide sequences of genes that are classified as
                       transposon-like
TE-LIKE_TRANSLATIONS.fasta
                     - Protein translations of genes that are classified as
                       transposon-like
PROTEIN-CODING_GENES.fasta
                     - Nucleotide sequences of genes that are classified as
                       having similarity to known proteins
PROTEIN-CODING_TRANSLATIONS.fasta
                     - Protein translations of genes that are classified as
                       having similarity to known proteins
HYPOTHETICAL_GENES.fasta
                     - Nucleotide sequences of genes that do not have 
                       similarity to any known protein
HYPOTHETICAL_TRANSLATIONS.fasta
                     - Protein translations of genes that do not have
                       similarity to any known protein
EVIDENCE_GENES.fasta
                     - Gene builds from biological evidence (ESTs, cDNAs..)
EVIDENCE_TRANSLATIONS.fasta
                     - Translations of Evidence based genes 

mysql/               - SQL dumps of the Ensembl maize databases used by the
                       browser
    zea_mays_core_49_bac_1a.sql.bz2: BAC sequences and underlying annotations
    zea_mays_core_49_fpc_1a.sql.bz2: The maize agarose FPC map
                              
NOTE ABOUT GENE TRANSLATIONS:
In the case of Fgenesh predictions (TE-LIKE, PROTEIN-CODING, and HYPOTHETICAL),
a small number of genes were predicted with stop-codons. This is an artifact of
Fgenesh predicting short genic fragments, often with singleton exons. We do not
include such translations in the file dumps.

Our website is located at:
    http://maizesequence.org

For more information, please contact us at:
    info@maizesequence.org

    
    
----
Last updated 2008-06-03