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to "Antoine Danchin" <antoine dot danchin at normalesup dot org>

>we are now analyzing nearly finished genome of Rhobacter capsulatus
>SB1003. I found at
>http://www.biomedcentral.com/content/pdf/1471-2105-8-47.pdf the article
>about Hon Yaku. We would like to apply your program/approach on our
>genome. Please, can you inform me, if it is possible and if it is, where
>we can find more information?

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reply:

Subject: Re: Hon Yaku
From: "Antoine Danchin" <antoine dot danchin et normalesup dot org>
Date: Sun, February 11, 2007 19:53
To: "Jan Paces" <hpaces at img dot cas dot cz>
Cc: ymakita at gsc dot riken dot jp
caudron at pasteur dot fr
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Dear colleague,

The best is that you contact Dr Yuko Makita, now at the Riken
Institute. The first step in your work will be to construct a
training set made of reference genes. However, before that, you could
use preset sets, and this should help you to get a fairly reliable
prediction of your CDSs starts. We plan in the near future, to set up
a Web service for the use of Hon-Yaku.

With my best wishes,

Yours
Antoine Danchin

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to Oymakita at gsc dot riken dot jp

I got your contact from Antoine Danchin (email attached below). We
would like, if possible, to apply yours Hon Yaku on our nearly finished
genome of the Rhodobacter capsulatus. Please, can you send me more
informations?

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reply:

Dear Jan,

Thank you very much for your query.
As Antoine mentioned before, you need to make training data set using
Rhodobacter capsulatus sequence.
(see p.11 of out manuscript, "Constructing data set with sequence
homology" )
Since Rhodobacter is a Proteobacteria, better to make a training data
set from the comparison with EcoGene data set.

If you (or the person who will actually run the script) are familiar
with Python, I can send my script to make a training data.
I will update the following URL, soon.

http://dbtbs.hgc.jp/Honyaku

Best wishes,
Yuko