The COGEME database has been updated with new sequences from Cladosporium
fulvum and Leptosphaeria maculans. The database now contains 26806
unisequences from 12 phytopathogens.
COGEME Fungal EST database: http://cogeme.ex.ac.uk
Mirror of COGEME database:
http://cbr-rbc.nrc-cnrc.gc.ca/services/cogeme/index.html
----------------------------------------------------------------------------
--------
Darren Soanes
School of Biological Sciences,
University of Exeter,
Washington Singer Laboratories,
Perry Road, Exeter, EX4 4QG, U.K.
Email: d.m.soanes@...
Tel: +44 (0)1392 264689
COGEME Fungal EST database: http://cogeme.ex.ac.uk
----------------------------------------------------------------------------
--------
[Non-text portions of this message have been removed]
Hi,
The COGEME database has been updated with more Magnaporthe grisea and
Gibberella zeae sequences. The database now contains 7245 M. grisea
sequences and 2403 G. zeae sequences, making a grand total of 26175
sequences. There are links to dbEST for unisequences made up from ESTs
downloaded from this database (that is all M. grisea, G. zeae, Phytophthora
and Colletotrichum trifolii sequences). The link is from the information
page for individual unisequences.
Best wishes,
Darren Soanes
COGEME Fungal EST database: http://cogeme.ex.ac.uk
----------------------------------------------------------------------------
--------
Darren Soanes
School of Biological Sciences,
University of Exeter,
Washington Singer Laboratories,
Perry Road, Exeter, EX4 4QG, U.K.
Email: d.m.soanes@...
Tel: +44 (0)1392 264689
COGEME Fungal EST database: http://cogeme.ex.ac.uk
----------------------------------------------------------------------------
--------
[Non-text portions of this message have been removed]
Hi,
there is now a mirror of the COGEME database hosted by the Canadian
Bioinformatics Resource.
It can be accessed at:
http://www.cbr.nrc.ca/services/cogeme/index.html
This might be useful if the Exeter server is down or running slowly.
Many thanks go to Sheldon Briand for his work in setting up the mirror site.
Darren Soanes
----------------------------------------------------------------------------
--------
Darren Soanes
School of Biological Sciences,
University of Exeter,
Washington Singer Laboratories,
Perry Road, Exeter, EX4 4QG, U.K.
Email: d.m.soanes@...
Tel: +44 (0)1392 264689
COGEME Fungal EST database: http://cogeme.ex.ac.uk
----------------------------------------------------------------------------
--------
[Non-text portions of this message have been removed]
Dear Officer
I would like to prospose the project 'AL in VR on Net'.
AL --Artificial Life
VR--Virtual Reality
NET --Internet
I'm searching anyone, any company, any organization
which collaborate with this project.
More detail, please see my home page 'www.geocities.com/alinvr_yyoshino'.
and Project Concept.
Just I would like to generate the clone in VR
and start next steps.
phase1: Visualization of Organ of Human body.
Shape,Color,Function, <--- Human Genome DB
Association Study, Designer Child,
BioProposal, MathProposal(Evolution theory,etc)
Phase2: Create Individual Character.
PsychoProposal.
Phase3: Contact the Clone.
I think this project is our mission and will develop worldwide.
For it regards with the culture and the tradition of each country.
On web I'd like to realize this project by interacting with
each specialists.
But I have not yet social capital and venture capital.
_________________________________________________________________
¥¦¥¤¥ë¥¹¥á¡¼¥ë¡¢ÌÂÏǥ᡼¥ëÂкö¤Ê¤é MSN Hotmail http://www.hotmail.com/
Hi,
550 unisequences from Colletotrichum trifolii have been added to the
COGEME fungal and oomycete EST database. The database now contains 22,806
sequences covering 10 species of phytopathogens.
Best wishes,
Darren Soanes
----------------------------------------------------------------------------
--------
Darren Soanes
School of Biological Sciences,
University of Exeter,
Washington Singer Laboratories,
Perry Road, Exeter, EX4 4QG, U.K.
Email: d.m.soanes@...
Tel: +44 (0)1392 264689
COGEME Fungal EST database: http://cogeme.ex.ac.uk
----------------------------------------------------------------------------
--------
[Non-text portions of this message have been removed]
Hi,
The COGEME fungal EST database (http://cogeme.ex.ac.uk) has been updated
with the addition of EST sequences from two oomycetes: 1414 unisequences
from Phytophthora infestans and 1384 unisequences from Phytophthora sojae,
making a total of 22256 sequences in the database.
There has also been some updates to the interface. For the two Phytophthora
species, it is now possible to link to a list showing which ESTs have been
assembled into a particular unisequence (from the unisequence information
page). For each individual EST there is a link to its dbEST record. This has
only so far been implemented for the Phytophthora species. In future updates
I will extend this to other unisequence sets that have been constructed from
ESTs deposited in dbEST. I have also revamped the information pages, giving
more info on the source of EST sets as well as some references.
Darren Soanes
----------------------------------------------------------------------------
--------
Darren Soanes
School of Biological Sciences,
University of Exeter,
Washington Singer Laboratories,
Perry Road, Exeter, EX4 4QG, U.K.
Email: d.m.soanes@...
Tel: +44 (0)1392 264689
COGEME Fungal EST database: http://cogeme.ex.ac.uk
----------------------------------------------------------------------------
--------
[Non-text portions of this message have been removed]
Hi Barry,
I have no plans to allow large scale BLASTs at the moment,
mainly because of the amount of server processor time it would take up. If
you want to do this then I can send you a FASTA file containing all the
sequences in the database (assuming your email account allows large
attachments, the sequence file is 12.7 Mb). You could then use the local
blast programs (downloadable from ftp://ftp.ncbi.nih.gov/blast/executables/)
to BLAST search the sequences on your own computer. Hope this is of some
help.
Darren
-----Original Message-----
From: bsaville@... [mailto:bsaville@...]
Sent: 17 August 2002 05:39
To: cogeme@...
Subject: [Cogeme] Searching Cogeme
Hello
I would like to know if you have are were going to set up Cogeme so that one
could take a new set of sequences (say another fungal EST library) and BLAST
it
against COGEME on mass say 100 sequence at a time?
Barry Saville
University of Toronto at MIssissauga
Yahoo! Groups Sponsor
To unsubscribe from this group, send an email to:
cogeme-unsubscribe@...
Your use of Yahoo! Groups is subject to the Yahoo! Terms of Service.
[Non-text portions of this message have been removed]
Hello
I would like to know if you have are were going to set up Cogeme so that one
could take a new set of sequences (say another fungal EST library) and BLAST it
against COGEME on mass say 100 sequence at a time?
Barry Saville
University of Toronto at MIssissauga
Hi,
I have now added 1455 Verticillium dahliae sequences to the COGEME
fungal EST database, making a grand total of 19,458 sequences.
Darren Soanes
----------------------------------------------------------------------------
--------
Darren Soanes
School of Biological Sciences,
University of Exeter,
Washington Singer Laboratories,
Perry Road, Exeter, EX4 4QG, U.K.
Email: d.m.soanes@...
Tel: +44 (0)1392 264689
COGEME Fungal EST database: http://cogeme.ex.ac.uk
----------------------------------------------------------------------------
--------
[Non-text portions of this message have been removed]
Thanks Darren.
R
-----Original Message-----
From: dmsoanes [mailto:d.m.soanes@...]
Sent: Monday, August 12, 2002 7:23 PM
To: cogeme@...
Subject: [Cogeme] Re: FW: Job openings at the ACNFP in Perth
Unfortunately this group doesn't allow email attachments to messages
posted. I have uploaded the advert to the files section of this
group. It can be accessed at:
http://uk.groups.yahoo.com/group/cogeme/files/Jobs%20flyer.doc
--- In cogeme@y..., "Richard Oliver" <roliver@c...> wrote:
>
>
>
>
> I'd be grateful if you could bring the attached ad the attention of
suitable
> candidates.
>
> Richard Oliver
> Australian Centre for Necrotrophic Fungal Pathogens
> DSE, South Street, Murdoch University
> WA 6150, Australia
> roliver@c...
> tel +61 (0)8 9360 7404
> fax +61 (0)8 9360 6303
> http://wwwacnfp.murdoch.edu.au/
>
>
> [Non-text portions of this message have been removed]
To unsubscribe from this group, send an email to:
cogeme-unsubscribe@...
Your use of Yahoo! Groups is subject to
http://uk.docs.yahoo.com/info/terms.html
Unfortunately this group doesn't allow email attachments to messages
posted. I have uploaded the advert to the files section of this
group. It can be accessed at:
http://uk.groups.yahoo.com/group/cogeme/files/Jobs%20flyer.doc
--- In cogeme@y..., "Richard Oliver" <roliver@c...> wrote:
>
>
>
>
> I'd be grateful if you could bring the attached ad the attention of
suitable
> candidates.
>
> Richard Oliver
> Australian Centre for Necrotrophic Fungal Pathogens
> DSE, South Street, Murdoch University
> WA 6150, Australia
> roliver@c...
> tel +61 (0)8 9360 7404
> fax +61 (0)8 9360 6303
> http://wwwacnfp.murdoch.edu.au/
>
>
> [Non-text portions of this message have been removed]
I'd be grateful if you could bring the attached ad the attention of suitable
candidates.
Richard Oliver
Australian Centre for Necrotrophic Fungal Pathogens
DSE, South Street, Murdoch University
WA 6150, Australia
roliver@...
tel +61 (0)8 9360 7404
fax +61 (0)8 9360 6303
http://wwwacnfp.murdoch.edu.au/
[Non-text portions of this message have been removed]
The COGEME website now contains a demonstration project written by MSc
student Peter Giles. It uses EST data from phytopathogenic fungi as an
indication to which amino acid biosynthesis pathways may be present in those
fungi. It can be accessed at:
http://cogeme.ex.ac.uk/biosynthesis.html
or by linking from the COGEME home page.
Darren Soanes
----------------------------------------------------------------------------
--------
Darren Soanes
School of Biological Sciences,
University of Exeter,
Washington Singer Laboratories,
Perry Road, Exeter, EX4 4QG, U.K.
Email: d.m.soanes@...
Tel: +44 (0)1392 264689
COGEME Fungal EST database: http://cogeme.ex.ac.uk
----------------------------------------------------------------------------
--------
[Non-text portions of this message have been removed]
Hi,
the COGEME database is now running normally and accessible from its
original URL: http://cogeme.ex.ac.uk
Sorry for any inconvenience caused by the site being offline in the last
couple of weeks.
Darren Soanes
----------------------------------------------------------------------------
--------
Darren Soanes
School of Biological Sciences,
University of Exeter,
Washington Singer Laboratories,
Perry Road, Exeter, EX4 4QG, U.K.
Email: d.m.soanes@...
Tel: +44 (0)1392 264689
COGEME Fungal EST database: http://cogeme.ex.ac.uk
----------------------------------------------------------------------------
--------
[Non-text portions of this message have been removed]
Hi,
those who have been trying to access the COGEME website in the last
couple of weeks will know that it has been inaccessible. This was due to the
resegmentation of the Exeter University computer network occuring at the
same time as I was away from the lab. It is now working again, though the
"cogeme.ex.ac.uk" URL is not working at the moment. In the meantime the
website is accessible from the following URL: http://obelix.ex.ac.uk/
The URL http://cogeme.ex.ac.uk should be working in a day or two.
Darren Soanes
----------------------------------------------------------------------------
--------
Darren Soanes
School of Biological Sciences,
University of Exeter,
Washington Singer Laboratories,
Perry Road, Exeter, EX4 4QG, U.K.
Email: d.m.soanes@...
Tel: +44 (0)1392 264689
COGEME Fungal EST database: http://cogeme.ex.ac.uk
----------------------------------------------------------------------------
--------
[Non-text portions of this message have been removed]
Hi,
the COGEME fungal EST database has been updated to version 1.2. After
running "search against putative product / function" or "advanced search"
queries it is now possible to retrieve a FASTA formated file containing all
the sequences returned by the query by clicking on "Retrieve sequences".
This opens a new window containing the sequences, which can be cut and
pasted into a text editor or saved directly from the browser window. The
BLAST interface has also changed slightly, when you run a BLAST search the
output now contains annotation about the unisequences as well as their
names. The webserver for the database has now changed from a PC running
"ZBserver" to a Sun workstation running Apache so it should be faster and
more stable. Any feedback would be welcome.
Darren Soanes
COGEME fungal EST database: http://cogeme.ex.ac.uk
----------------------------------------------------------------------------
Darren Soanes
School of Biological Sciences,
University of Exeter,
Washington Singer Laboratories,
Perry Road, Exeter, EX4 4QG.
Email: d.m.soanes@...
Tel: +44 (0)1392 264689
----------------------------------------------------------------------------
[Non-text portions of this message have been removed]
Hi,
Version 1.1 of COGEME Fungal EST database has been released. The
database website now features an advanced search query that enables the user
to perform more sophisticated searches of the putative functions of
sequences in the database, including the ability to search by functional
classification group. The advanced search page can be reached at:
http://cogeme.ex.ac.uk/advsearch.html
or by a link from the home page of the database:
http://cogeme.ex.ac.uk
Darren Soanes
----------------------------------------------------------------------------
Darren Soanes
School of Biological Sciences,
University of Exeter,
Washington Singer Laboratories,
Perry Road, Exeter, EX4 4QG.
Email: d.m.soanes@...
Tel: +44 (0)1392 264689
----------------------------------------------------------------------------
[Non-text portions of this message have been removed]
Hi,
there have been more Magnaporthe grisea EST sequences added to the
COGEME fungal EST database (http://cogeme.ex.ac.uk/). The database now
contains 18002 EST sequences in total, 5142 of which are from M. grisea.
Cheers, Darren
----------------------------------------------------------------------------
Darren Soanes
School of Biological Sciences,
University of Exeter,
Washington Singer Laboratories,
Perry Road, Exeter, EX4 4QG.
Email: d.m.soanes@...
Tel: +44 (0)1392 264689
----------------------------------------------------------------------------
[Non-text portions of this message have been removed]
Hi,
New Magnaporthe grisea sequences have been added to the COGEME
fungal EST database (http://cogeme.ex.ac.uk/). The database now
contains 3161 M. grisea sequences and 16018 sequences in total. There
has also been a minor update to the BLAST interface. As always any
feedback would be welcome.
Darren Soanes
Hi,<br> 3238 Fusarium sporotrichioides EST
sequences have been added to the COGEME fungal EST database
(<a href=http://cogeme.ex.ac.uk/ target=new>http://cogeme.ex.ac.uk/</a>), making
a total of 14695. Any comments or feedback
would be welcome.<br>Darren Soanes
Hi,<br> 2852 Botryotinia fuckeliana (Botrytis
cinerea) EST sequences have been added to the COGEME
fungal EST database (<a href=http://cogeme.ex.ac.uk/
target=new>http://cogeme.ex.ac.uk/</a>), making a
total of 11455. Please take a look, any feedback would
be welcome.<br><br>Darren Soanes
Hi,<br> the COGEME fungal EST database has been
updated with extra M.grisea and M.graminicola sequences.
The database now contains 2926 M.graminicola, 1839
M.grisea and 2701 B.graminis unisequences. If you find any
mistakes please point them out to me so they can be
corrected in the next update.<br>Cheers, Darren
There are quite a lot of glitches with this
database, so when I get back from holiday I will sort it
out. In the meantime I've removed the link from the
mainpage. You can still use the direct link, but it is
unlikely to work on anything except a PC running Internet
Explorer.
Hi,<br> as part of an Bioinformatics MSc project,
Peter Giles has created an "Amino Acid Biosynthesis
Gene Discovery Database for<br>Pathogenic Fungi".This
can be accessed by a link from the Exeter Cogeme
homepage or directly
at:<br><a href=http://cogeme.ex.ac.uk/biosynthesis.html
target=new>http://cogeme.ex.ac.uk/biosynthesis.html</a><br><br>I haven't fully
checked it out for bugs / browser
compatibility yet (I will after I get back from holiday in two
weeks), and its a bit lacking in documentation, but check
it out, its very good.<br><br>Cheers, Darren
After a request from a user I have altered the
blast search page in the database so you can turn
on/off the low complexity filter. By default it is on
which should be suitable for most searches.<br>Darren
Hi,<br> you should now be able to access the
Cogeme database from outside Exeter Uni. The network
admin had typed in our IP address wrongly and he was on
holiday last week so he only changed it today. So
hopefully everything should be fine. There is also a
revamped Talbot lab page that is actually up to date
(first time in about three years). It is available at
<a href=http://www.ex.ac.uk/biology/talbot
target=new>http://www.ex.ac.uk/biology/talbot</a><br> Darren
The database is working fine, except it is
unreachable apart from inside the university at the moment.
To increase security the University has blocked
access to all University computers from outside the
campus, except named servers. Ours is supposedly one of
these, except access is still blocked (as it is to the
Bioinformatics server). Hopefully it will be sorted out
soon.<br>Sorry for an inconvenience.<br> Darren
Hi,<br> I've now fixed a bug in the Perl scripts
which meant the website didn't display properly on
Internet Explorer for the Mac. So Mac lovers rejoice you
can use our database.<br> Darren
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