From gbottu at ben.vub.ac.be  Thu Sep 18 05:32:22 2003
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Thu, 18 Sep 2003 11:32:22 +0200 (CEST)
Subject: Staden format (again)
Message-ID: <200309180932.h8I9WMQ81418856@black.vub.ac.be>

from : BEN

	Dear friends,
	
Excuse me if I am beating a dead horse. I took a look at EMBOSS 2.7.1 and I saw 
that Staden and experiment format are still not handled correctly.

Staden format : actually obsolete, the latest version of the Staden package does 
not support it anymore. Staden format is a just the sequence in simple text 
with, optionally, comments  <xxxxx>  at any position in the sequence. When 
EMBOSS reads in "staden" format, it recognizes only a comment at the top of the 
sequence but considers comments inside the sequence as part of the sequence.

Staden experiment format : is used by Staden for assembly. Looks like EMBL 
format, but with a lot of extra fields related to the DNA sequencing, and only  
one sequence per file is allowed, there can be fields below the "//". EMBOSS 
erroneously uses "experiment" as synonym for "staden". You can find more 
information about "experiment" format at
http://www.mrc-lmb.cam.ac.uk/pubseq/manual/formats_unix_18.html

	Sincerely,
	Guy Bottu


From pmr at ebi.ac.uk  Thu Sep 18 06:11:28 2003
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 18 Sep 2003 11:11:28 +0100
Subject: Sequence formats (was: Staden format (again))
References: <200309180932.h8I9WMQ81418856@black.vub.ac.be>
Message-ID: <3F6984D0.403@ebi.ac.uk>

Guy Bottu wrote:
> from : BEN

(Belgian EMBnet Node for the uninitiated :-)
  	
> Excuse me if I am beating a dead horse. I took a look at EMBOSS 2.7.1 and I saw 
> that Staden and experiment format are still not handled correctly.
> 
> Staden format : actually obsolete, the latest version of the Staden package does 
> not support it anymore. Staden format is a just the sequence in simple text 
> with, optionally, comments  <xxxxx>  at any position in the sequence. When 
> EMBOSS reads in "staden" format, it recognizes only a comment at the top of the 
> sequence but considers comments inside the sequence as part of the sequence.

I'll take a look. It is a little tricky. GCG use the same comments (does 
anyone still use them? you could insert them using the seqed editor) so 
the GCG format needs the same change. Basically, in the sequence 
anything after < is a comment until a > is found, possibly on a later line.

This reminds me of a sequence I once saw that GCG failed to read - 
because it had been cut and pasted in an email, and had a '<' character 
at the start of a line so the rest was commented out :-)

> Staden experiment format : is used by Staden for assembly. Looks like EMBL 
> format, but with a lot of extra fields related to the DNA sequencing, and only  
> one sequence per file is allowed, there can be fields below the "//". EMBOSS 
> erroneously uses "experiment" as synonym for "staden". You can find more 
> information about "experiment" format at
> http://www.mrc-lmb.cam.ac.uk/pubseq/manual/formats_unix_18.html

Thanks. I will take a look.

Does anyone have real examples of these formats?

Does anyone have real examples of any other formats EMBOSS supports?

Does anyone have real examples of any formats EMBOSS dioes not (yet) 
support?

regards,

Peter Rice





From ursuckaz19380nadcost at yahoo.com  Tue Sep 23 10:44:11 2003
From: ursuckaz19380nadcost at yahoo.com (Betty)
Date: Tue, 23 Sep 2003 07:44:11 -0700
Subject: test my livecam please
Message-ID: <2003092528.7040.qmail@yahoo.com>

Hi Eric !

I am doing something I never thought I would do. 
Because I need some money (you know that I'am
a student ;-) ) I will start my own nude livecam 
next week.

The webcam is already online and it would be
great if you could test the performane of
my cam:
http://betty.my-free-website.com

There is also a chat - please test this
too. Of course I will do all you want.....
Just tell me via chat what you want
to see:
http://betty.my-free-website.com

Your test should be something like a 
"real customer simulation" ;-) 

What are you doing this summer ?

Yours,
Betty
http://betty.my-free-website.com



From raouljp at libero.it  Wed Sep 24 05:04:46 2003
From: raouljp at libero.it (raouljp at libero.it)
Date: Wed, 24 Sep 2003 11:04:46 +0200
Subject: Qualifier
Message-ID: <HLPNVY$5C26D5001F5129532C34EAE7D85FD605@libero.it>

hi,
I think would be useful that user, from ACD file, can add personal qualifier. In
reality I need this functionality so, is there a way to add personal qualifier ?
Where is it the piece of code I should hack ?

by RJP



From pmr at ebi.ac.uk  Wed Sep 24 05:47:39 2003
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 24 Sep 2003 10:47:39 +0100
Subject: Qualifier
References: <HLPNVY$5C26D5001F5129532C34EAE7D85FD605@libero.it>
Message-ID: <3F71683B.30202@ebi.ac.uk>

raouljp at libero.it wrote:
> hi,
> I think would be useful that user, from ACD file, can add personal qualifier. In
> reality I need this functionality so, is there a way to add personal qualifier ?
> Where is it the piece of code I should hack ?

Can you give an example of what you want?

regards,

Peter Rice




From gbottu at ben.vub.ac.be  Thu Sep 18 09:32:22 2003
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Thu, 18 Sep 2003 11:32:22 +0200 (CEST)
Subject: Staden format (again)
Message-ID: <200309180932.h8I9WMQ81418856@black.vub.ac.be>

from : BEN

	Dear friends,
	
Excuse me if I am beating a dead horse. I took a look at EMBOSS 2.7.1 and I saw 
that Staden and experiment format are still not handled correctly.

Staden format : actually obsolete, the latest version of the Staden package does 
not support it anymore. Staden format is a just the sequence in simple text 
with, optionally, comments  <xxxxx>  at any position in the sequence. When 
EMBOSS reads in "staden" format, it recognizes only a comment at the top of the 
sequence but considers comments inside the sequence as part of the sequence.

Staden experiment format : is used by Staden for assembly. Looks like EMBL 
format, but with a lot of extra fields related to the DNA sequencing, and only  
one sequence per file is allowed, there can be fields below the "//". EMBOSS 
erroneously uses "experiment" as synonym for "staden". You can find more 
information about "experiment" format at
http://www.mrc-lmb.cam.ac.uk/pubseq/manual/formats_unix_18.html

	Sincerely,
	Guy Bottu


From pmr at ebi.ac.uk  Thu Sep 18 10:11:28 2003
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 18 Sep 2003 11:11:28 +0100
Subject: Sequence formats (was: Staden format (again))
References: <200309180932.h8I9WMQ81418856@black.vub.ac.be>
Message-ID: <3F6984D0.403@ebi.ac.uk>

Guy Bottu wrote:
> from : BEN

(Belgian EMBnet Node for the uninitiated :-)
  	
> Excuse me if I am beating a dead horse. I took a look at EMBOSS 2.7.1 and I saw 
> that Staden and experiment format are still not handled correctly.
> 
> Staden format : actually obsolete, the latest version of the Staden package does 
> not support it anymore. Staden format is a just the sequence in simple text 
> with, optionally, comments  <xxxxx>  at any position in the sequence. When 
> EMBOSS reads in "staden" format, it recognizes only a comment at the top of the 
> sequence but considers comments inside the sequence as part of the sequence.

I'll take a look. It is a little tricky. GCG use the same comments (does 
anyone still use them? you could insert them using the seqed editor) so 
the GCG format needs the same change. Basically, in the sequence 
anything after < is a comment until a > is found, possibly on a later line.

This reminds me of a sequence I once saw that GCG failed to read - 
because it had been cut and pasted in an email, and had a '<' character 
at the start of a line so the rest was commented out :-)

> Staden experiment format : is used by Staden for assembly. Looks like EMBL 
> format, but with a lot of extra fields related to the DNA sequencing, and only  
> one sequence per file is allowed, there can be fields below the "//". EMBOSS 
> erroneously uses "experiment" as synonym for "staden". You can find more 
> information about "experiment" format at
> http://www.mrc-lmb.cam.ac.uk/pubseq/manual/formats_unix_18.html

Thanks. I will take a look.

Does anyone have real examples of these formats?

Does anyone have real examples of any other formats EMBOSS supports?

Does anyone have real examples of any formats EMBOSS dioes not (yet) 
support?

regards,

Peter Rice





From ursuckaz19380nadcost at yahoo.com  Tue Sep 23 14:44:11 2003
From: ursuckaz19380nadcost at yahoo.com (Betty)
Date: Tue, 23 Sep 2003 07:44:11 -0700
Subject: test my livecam please
Message-ID: <2003092528.7040.qmail@yahoo.com>

Hi Eric !

I am doing something I never thought I would do. 
Because I need some money (you know that I'am
a student ;-) ) I will start my own nude livecam 
next week.

The webcam is already online and it would be
great if you could test the performane of
my cam:
http://betty.my-free-website.com

There is also a chat - please test this
too. Of course I will do all you want.....
Just tell me via chat what you want
to see:
http://betty.my-free-website.com

Your test should be something like a 
"real customer simulation" ;-) 

What are you doing this summer ?

Yours,
Betty
http://betty.my-free-website.com



From raouljp at libero.it  Wed Sep 24 09:04:46 2003
From: raouljp at libero.it (raouljp at libero.it)
Date: Wed, 24 Sep 2003 11:04:46 +0200
Subject: Qualifier
Message-ID: <HLPNVY$5C26D5001F5129532C34EAE7D85FD605@libero.it>

hi,
I think would be useful that user, from ACD file, can add personal qualifier. In
reality I need this functionality so, is there a way to add personal qualifier ?
Where is it the piece of code I should hack ?

by RJP



From pmr at ebi.ac.uk  Wed Sep 24 09:47:39 2003
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 24 Sep 2003 10:47:39 +0100
Subject: Qualifier
References: <HLPNVY$5C26D5001F5129532C34EAE7D85FD605@libero.it>
Message-ID: <3F71683B.30202@ebi.ac.uk>

raouljp at libero.it wrote:
> hi,
> I think would be useful that user, from ACD file, can add personal qualifier. In
> reality I need this functionality so, is there a way to add personal qualifier ?
> Where is it the piece of code I should hack ?

Can you give an example of what you want?

regards,

Peter Rice