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Genome Reviews News
News
02/10/2007
New annotations for non-protein-coding RNA genes have been added to
Genome Reviews entries
where the original submission does not contain any such annotation,
using a similar approach
to that already used for tRNA genes. The program rfam_scan.pl has been
applied
to the DNA sequence of such entries, and new annotations have been added
according to the results.
rfam_scan.pl is a perl wrapper for searching DNA sequence against the
latest Rfam Database
Griffiths-Jones S. et al. (2005)) using the INFERNAL software package
(Eddy, S.R. (2002)).
Full details of these changes are provided in section 4 of the user manual.
There is also a change in the gene_name qualifier of tRNA features.
Thymines (T) were replaced by Uridines (U).
11/9/2007
The 23 chromosomes of the filamentous fungus Ustilago maydis strain 521
have been added to Genome Reviews. The underlying sequence is the first
release of the high-quality draft sequence from the Broad Institute.
Genome Reviews records were built from annotated sequence records
constructed at MIPS (http://mips.gsf.de/) as part of their Ustilago
maydis Annotation Project.
16/5/2007
From release 73 the Gene Sets for archaea, bacteria and phage are
available through EBI SRS (srs.ebi.ac.uk). See user manual
sections 5 and 6.2 for details.
Hosts and host ranges curated from the scientific literature have
been added to all phage records.
The Arabidopsis records now include data from the new TAIR release
(Release 7).
6/3/2007
From Release 69 onwards, the Genome Reviews database includes the
genomes of bacteriophage. For clarity we now present the flat files
in two sections: cellular and bacteriophage genomes. These can be
downloaded by following the links on the Genome Reviews home page or via
ftp as described in the user manual and the release notes.
In addition, gene records are now available for all archaeal and bacterial
genomes in Genome Reviews. Each record represents one gene present in a
Genome Reviews component record; records are available for download as
sets comprising the genes present in one component, and the genes
present in one genome. The file format is the same as used for EMBL CDS records and is described in the Genome Reviews user manual. See section
3.1 (b) of this document for information about accessing the gene sets.
14/11/2006
From release 62.0 data from RegulonDB (http://regulondb.ccg.unam.mx/) is incorporated into Genome Reviews entry U00096_GR (E.coli strain K12).
We have introduced a number of additional features and qualifiers to
accommodate this data. Please see the latest
Release Notes
for additional information.
4/10/2006
From release 59.0 Genome Reviews contains the complete genomes of two
additional eukaryotes, the fungal pathogen Cryptococcus neoformans strain
JEC21, the causative agent of cryptococcosis (the most
common clinical form is meningoencephalitis) and the
microsporidian pathogen Encephalitozoon cuniculi strain GB-M1, which
causes diarrhea and respiratory problems.
7/2/2006
Arabidopsis thaliana genome added to the Genome Reviews database
From release 44.0 we are including the complete genome of
Arabidopsis thaliana (thale cress) in the Genome Reviews
database.
The source for
chromosomes 1 to 5 and the mitochondrial chromosome is taken from
TAIR's
latest genome release; the source for the chloroplast genome is
EMBL database entry AP000423.
Genome Reviews mailing list
We encourage users who wish to be kept informed about changes and new
developments to subscribe
to the new Genome Reviews mailing list genomereviews-announce@ebi.ac.uk at
URL:
http://listserver.ebi.ac.uk/mailman/listinfo/genomereviews-announce.
Previous postings to the
mailing list can be viewed through the link Genomereviews-announce
Archives on the same page.
13/5/2005
Genome Reviews MySQL database export file available from ftp server
Starting with release 26.0 we provide an export of the current Genome
Reviews release from a MySQL database. The data corresponds to the same
data found in the flat file distribution and the database schema is
essentially the same as that used by Ensembl to describe higher eukaryotic
genomes. See section 5.2 of the user manual for further
details... more
24/10/2005
Genome Reviews Browser released
See top of the page for further information.
27/9/2005
Inclusion of first lower eukaryotic genome in Genome Reviews
From release 36.0, Genome Reviews includes a representation of the
genome of the eukaryote Saccharomyces cerevisiae. The source
sequences are taken from the Saccharomyces Genome Database (SGD).
13/5/2005
Genome Reviews MySQL database export file available from ftp server
Starting with release 26.0 we provide an export of the current Genome
Reviews release from a MySQL database. The data corresponds to the same
data found in the flat file distribution and the database schema is
essentially the same as that used by Ensembl to describe higher eukaryotic
genomes. See section 5.2 of the user manual for further
details... more
28/02/2005
Annotations for "missing" protein and tRNA-encoding genes added.
Annotations for tRNA-coding genes have been added to all Genome Reviews entries where the original EMBL submission did not contain any such annotations. In addtion, annotations for protein-coding sequiences corresponding to UniProt entries that were not originally annotated have been added by mapping the protein sequence against the corresponding genome. See section 4 of the user manual for more details |
21/06/2004
Cross references to HOGENOM added.
HOGENOM is a resource to enable comparative phylogenetics of species with completely deciphered genomes. |
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 This project has been funded by the European Commission: from March 2006 -
February 2009 under FELICS, contract number 021902 (RII3)
within the
Research Infrastructure Action of the FP6
"Structuring the European
Research Area" Programme
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