p_func component obsolete?

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p_func component obsolete?

ML mail
Dear Ergatis users,

I am currently planning to run the "Prokaryotic Annotation Pipeline Without
Loading" global template and noticed that one of the last components, p_func,
looks outdated to be: it uses TIGR roles database (as defined in
software.config) which somehow doesn't look to exist anymore or has been renamed
to TIGRFAM. I am saying something wrong here or am I right that TIGR roles
database is obsolete?

If it is obsolete would it be possible to simply delete this component from the
pipeline without affecting the results? Or is there maybe a new component which
does the same task and which I can replace with?

Thanks for your input.
Regards


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Re: p_func component obsolete?

Kevin Galens
The pFunc component is an integral part of the Prokaryotic Annotation
Pipeline. This component is responsible for assigning the functional
annotations to all the polypeptides. The ROLES_DB_DIR which pFunc needs
during configuration is the path the directory which contains a file that
defines lookup from various keywords to TIGR roles ids. pFunc will assign
TIGR roles to unassigned proteins based on predicted common names using
this file. We have our own file here I can send to you.

Kevin Galens
[hidden email]

On 5/6/11 11:08 AM, "ML mail" <[hidden email]> wrote:

>Dear Ergatis users,
>
>I am currently planning to run the "Prokaryotic Annotation Pipeline
>Without
>Loading" global template and noticed that one of the last components,
>p_func,
>looks outdated to be: it uses TIGR roles database (as defined in
>software.config) which somehow doesn't look to exist anymore or has been
>renamed
>to TIGRFAM. I am saying something wrong here or am I right that TIGR
>roles
>database is obsolete?
>
>If it is obsolete would it be possible to simply delete this component
>from the
>pipeline without affecting the results? Or is there maybe a new component
>which
>does the same task and which I can replace with?
>
>Thanks for your input.
>Regards
>
>
>--------------------------------------------------------------------------
>----
>WhatsUp Gold - Download Free Network Management Software
>The most intuitive, comprehensive, and cost-effective network
>management toolset available today.  Delivers lowest initial
>acquisition cost and overall TCO of any competing solution.
>http://p.sf.net/sfu/whatsupgold-sd
>_______________________________________________
>Ergatis-users mailing list
>[hidden email]
>https://lists.sourceforge.net/lists/listinfo/ergatis-users



------------------------------------------------------------------------------
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management toolset available today.  Delivers lowest initial
acquisition cost and overall TCO of any competing solution.
http://p.sf.net/sfu/whatsupgold-sd
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Re: p_func component obsolete?

ML mail
Dear Kevin,

Many thanks for your detailed information regarding the pFunc component in
Ergatis. It would be really great if you could send me your own TIGR roles files
or just let me know where I can download it. Yesterday, I was looking through
the whole FTP server of the JCVI (ftp.jcvi.org) but couldn't find anything...

Regards,
ML


----- Original Message ----
From: Kevin Galens <[hidden email]>
To: [hidden email]
Sent: Fri, May 6, 2011 4:53:07 PM
Subject: Re: [Ergatis-users] p_func component obsolete?

The pFunc component is an integral part of the Prokaryotic Annotation
Pipeline. This component is responsible for assigning the functional
annotations to all the polypeptides. The ROLES_DB_DIR which pFunc needs
during configuration is the path the directory which contains a file that
defines lookup from various keywords to TIGR roles ids. pFunc will assign
TIGR roles to unassigned proteins based on predicted common names using
this file. We have our own file here I can send to you.

Kevin Galens
[hidden email]

On 5/6/11 11:08 AM, "ML mail" <[hidden email]> wrote:

>Dear Ergatis users,
>
>I am currently planning to run the "Prokaryotic Annotation Pipeline
>Without
>Loading" global template and noticed that one of the last components,
>p_func,
>looks outdated to be: it uses TIGR roles database (as defined in
>software.config) which somehow doesn't look to exist anymore or has been
>renamed
>to TIGRFAM. I am saying something wrong here or am I right that TIGR
>roles
>database is obsolete?
>
>If it is obsolete would it be possible to simply delete this component
>from the
>pipeline without affecting the results? Or is there maybe a new component
>which
>does the same task and which I can replace with?
>
>Thanks for your input.
>Regards
>
>
>--------------------------------------------------------------------------
>----
>WhatsUp Gold - Download Free Network Management Software
>The most intuitive, comprehensive, and cost-effective network
>management toolset available today.  Delivers lowest initial
>acquisition cost and overall TCO of any competing solution.
>http://p.sf.net/sfu/whatsupgold-sd
>_______________________________________________
>Ergatis-users mailing list
>[hidden email]
>https://lists.sourceforge.net/lists/listinfo/ergatis-users



------------------------------------------------------------------------------
WhatsUp Gold - Download Free Network Management Software
The most intuitive, comprehensive, and cost-effective network
management toolset available today.  Delivers lowest initial
acquisition cost and overall TCO of any competing solution.
http://p.sf.net/sfu/whatsupgold-sd
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users


------------------------------------------------------------------------------
WhatsUp Gold - Download Free Network Management Software
The most intuitive, comprehensive, and cost-effective network
management toolset available today.  Delivers lowest initial
acquisition cost and overall TCO of any competing solution.
http://p.sf.net/sfu/whatsupgold-sd
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users