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Phytopathogenic Fungi and Oomycete EST Database

Version 1.6


Sequences

In order to reduce sequence redundancy, sequence assembly software was used to join together EST sequences representing the same gene into a single contig or consensus sequence. The unisequence set for each pathogen therefore represents a set of unique gene sequences, each one consisting of either a single EST (singleton) or a contig sequence made from a group of ESTs. For more information on the source of ESTs for each organism click on the links below.


   Alternaria brassicicola
   Aspergillus niger
   Blumeria graminis
   Botryotinia fuckeliana
   Cladosporium fulvum
   Colletotrichum gloeosporioides f. sp. aeschynomene
   Colletotrichum trifolii
   Cryphonectria parasitica
   Emericella nidulans
   Fusarium sporotrichioides
   Gibberella zeae
   Glomerella cingulata
   Leptosphaeria maculans
   Magnaporthe grisea
   Mycosphaerella graminicola
   Neurospora crassa
   Ophiostoma novo-ulmi
   Phaeosphaeria nodorum
   Phytophthora infestans
   Phytophthora sojae
   Sclerotinia sclerotiorum
   Ustilago maydis
   Verticillium dahliae

Sequence Annotation

To ascertain putative gene products for each unisequence, the NCBI database was queried for hits against the unisequences using the blastx algorithm (Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ : J Mol Biol 1990 Oct 5;215(3):403-10). The top hits (with e-values less than 1 x 10-5) for each unisequence have been entered into the database. On the basis of these hits a putative product / function was assigned to each unisequence. There is no experimental evidence for these assignments, so some of them are speculative. Based on these assignments, the unisequences were classified by function according to a scheme adapted from that used by MIPS (Munich Information Centre for Protein Sequences). Click here to view the functional classification scheme.

Database and Website Implementation

The relational database was implemented using MySQL version 3.23.28 for Solaris. Web-based database searching was implemented with CGI-Perl scripts (Perl 5.6.1) using Perl modules DBI and DBD-Mysql. To allow BLAST searching of the unisequence dataset, the BLAST suite of programs were downloaded from the NCBI BLAST ftp site. A web page and CGI-Perl script was written to implement the user interface with the BLAST programs. The website and database is hosted on a Sun Ultra 10 workstation running Apache 2.0.36. Once transcriptome data is available for the unisequences this will be added. Any comments or suggestions are welcome, especially if you spot any errors.

History

06/08/2001 Version 1.0 of the database online.
07/11/2001 New M. graminicola and M. grisea sequences added.
14/12/2001 Gibberella zeae sequences added.
28/01/2002 Botryotinia fuckeliana sequences added.
22/02/2002 Fusarium sporotrichioides sequences added.
21/03/2002 New Magnaporthe grisea sequences added.
26/04/2002 New Magnaporthe grisea sequences added.
03/05/2002 Version 1.1 released, advanced search query added.
30/05/2002 Version 1.2 released, sequence retrieval added.
16/08/2002 Verticillium dahliae sequences added.
20/09/2002 Phytophthora sequences added.
15/10/2002 Colletotrichum trifolii sequences added.
19/12/2002 New G. zeae and M. grisea sequences added.
13/02/2003 C. fulvum and L. maculans sequences added.
25/03/2003 Version 1.3 released, analysis of EST transcript abundance added.
19/05/2003 Unisequence sets can now be downloaded.
19/05/2003 B. fuckeliana and F. sporotrichioides sequences reassembled.
04/08/2003 New Magnaporthe grisea sequences added.
15/09/2003 Cryphonectria parasitica sequences added.
30/09/2003 Version 1.4 released, hits against yeast genes added.
08/12/2003 Sclerotinia sclerotiorum sequences added.
08/12/2003 New P. sojae sequences added.
19/02/2004 Ustilago maydis sequences added.
19/02/2004 New B. graminis and G. zeae sequences added.
04/06/2004 A. niger, E.nidulans and N.crassa sequences added
04/06/2004 New B. graminis sequences added.
08/06/2004 Version 1.5 released, functions related to individual ESTs added.
21/12/2004 New Magnaporthe grisea sequences added.
07/02/2006 New G. zeae and P. sojae sequences added.
23/05/2006 New E. nidulans sequences added.
04/09/2007 Version 1.6 released, sequences from five new species added.

Darren Soanes, University of Exeter. Email: d.m.soanes@exeter.ac.uk