ATH1 Data Release 3.0 from TIGR

Town, Christopher ChrisD. cdtown at tigr.org
Fri Aug 2 10:18:59 EST 2002


The Arabidopsis bioinformatics team at TIGR is pleased to announce 
Release 3.0 of the Arabidopsis genome annotation. Here are some 
statistics for the new release:



5 chromosomes totaling 117.3 M bp

Tiling path consisting of 1578 BACs (includes PCR products and

MIPS-contigs)

Annotation containing 27117 protein coding genes and 1967 pseudogenes



There are 10569 gene models supported by complete cDNAs.



4291 genes have been manually curated with Gene Ontology assignments.



In comparison to Release 2.0 back in January, there are 1623 new gene 
annotations:   

993 of these are protein coding genes:

          52 of these are supported by complete cDNAs

         108 have EST but not FL-cDNA matches

         592 have no Arabidopsis cDNA or EST support but have a match 
to the TIGR non-redundant protein database

630 of the new genes are pseudogenes



Also in comparison to Release 2.0, at least 1446 gene models were 
updated to encode different protein sequences. 880 of these genes are 
supported by complete cDNAs.



This latest annotation can be viewed at 
<http://www.tigr.org/>www.tigr.org and will also be incorporated into 
the displays at TAIR and GenBank.



All data associated with Arabidopsis Data Release 3.0 and are 
available on our FTP site.  The annotation data are provided on the 
TIGR FTP site in XML for the individual BACs and at the chromosome 
level.  ASN1-formatted files for the chromosome-based annotation for 
representation in NCBI's Genome database are also provided.

<ftp://ftp.tigr.org/pub/data/a_thaliana/ath1/PSEUDOCHROMOSOMES/>ftp://ftp.tigr.org/pub/data/a_thaliana/ath1/PSEUDOCHROMOSOMES/



The BAC-based XML is only being provided for the BACS which are built 
into the tiling path and used for chromosome construction.

<ftp://ftp.tigr.org/pub/data/a_thaliana/ath1/BACS/>ftp://ftp.tigr.org/pub/data/a_thaliana/ath1/BACS/



FASTA sequences are provided for proteins, CDS sequences, and the 
unspliced transcript sequences for each gene, as well as the BACs and 
the newly constructed chromosome sequences.

<ftp://ftp.tigr.org/pub/data/a_thaliana/ath1/SEQUENCES/>ftp://ftp.tigr.org/pub/data/a_thaliana/ath1/SEQUENCES/



Lists of genes supported by full-length cDNAs, genes new in release 
3.0 and genes updated in release 3.0: 
<ftp://ftp.tigr.org/pub/data/a_thaliana/ath1/DATA_RELEASE_SUPPLEMENT/>ftp://ftp.tigr.org/pub/data/a_thaliana/ath1/DATA_RELEASE_SUPPLEMENT/





__________________________________

Chris Town

Associate Investigator

The Institute for Genomic Research

9712 Medical Center Drive

Rockville, MD 20850



Phone: 301-838-3523

Fax: 301-838-0208

To page me at TIGR: 301-838-0200







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