question about the BLC format

Jalview Discussion
1

Hi Jim & al.,
I'm looking for any kind of documentation regarding the BLC alignment format which is supported by Jalview (I'm looking to register this format in EDAM ontology). Is there somewhere a specification for this format?
Best,
Hervé

2

Hi Hervé.

The best documentation source is here:
http://www.compbio.dundee.ac.uk/manuals/scanps/subsection3_15_2.html

Jalview supports access to any of the iterations - when reading a BLC file, you can put a '#<iteration number>' after the filename to select which iteration you want to import as an alignment. The BLC comment section is imported and shown from the Alignment properties dialog.

Is that sufficient ? Or should we encourage Geoff to put up a more detailed example :wink:

Jim.

Quoting "Hervé Ménager" <hmenager@pasteur.fr>:

···

Hi Jim & al.,
I'm looking for any kind of documentation regarding the BLC alignment
format which is supported by Jalview (I'm looking to register this
format in EDAM ontology). Is there somewhere a specification for this
format?
Best,
Hervé
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

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3

Good afternoon
I was wondering if there is a simple way to avoid the Jalview from showing a bunch of illustrative ways to use the data every time it starts up. These have to be closed before going to the real work.

Peter

···

Date: Tue, 22 Oct 2013 17:18:00 +0100
From: jprocter@compbio.dundee.ac.uk
To: jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] question about the BLC format

Hi Hervé.

The best documentation source is here:
http://www.compbio.dundee.ac.uk/manuals/scanps/subsection3_15_2.html

Jalview supports access to any of the iterations - when reading a BLC
file, you can put a ‘#’ after the filename to select
which iteration you want to import as an alignment. The BLC comment
section is imported and shown from the Alignment properties dialog.

Is that sufficient ? Or should we encourage Geoff to put up a more
detailed example :wink:

Jim.

Quoting “Hervé Ménager” hmenager@pasteur.fr:

Hi Jim & al.,
I’m looking for any kind of documentation regarding the BLC alignment
format which is supported by Jalview (I’m looking to register this
format in EDAM ontology). Is there somewhere a specification for this
format?
Best,
Hervé

Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

This message was sent using IMP, the Internet Messaging Program.

Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

4

Actually, I already answered this, but forgot to copy to the list: Here is my version:

Hervé

Yes, this is defined in the documentation to the AMPS package for multiple alignment. You can read the description on-line here:

http://www.compbio.dundee.ac.uk/manuals/amps/subsubsection3_18_2_5.html#SECTION00018250000000000000

AMPS together with its documentation can be downloaded from here:

http://www.compbio.dundee.ac.uk/downloads/amps/

The blc file format is also used by some other older programs from my group (e.g. STAMP) since it allows additional information to be encoded after the sequences without destroying the ability for programs to read the amino acid sequences. For example, STAMP encodes information about structural similarity and AMAS outputs measures of conservation which are floating point numbers in an additional column.

Geoff.

···

On 22/10/2013 17:18, Jim Procter wrote:

Hi Hervé.

The best documentation source is here:
http://www.compbio.dundee.ac.uk/manuals/scanps/subsection3_15_2.html

Jalview supports access to any of the iterations - when reading a BLC
file, you can put a '#<iteration number>' after the filename to select
which iteration you want to import as an alignment. The BLC comment
section is imported and shown from the Alignment properties dialog.

Is that sufficient ? Or should we encourage Geoff to put up a more
detailed example :wink:

Jim.

Quoting "Hervé Ménager" <hmenager@pasteur.fr>:

Hi Jim & al.,
I'm looking for any kind of documentation regarding the BLC alignment
format which is supported by Jalview (I'm looking to register this
format in EDAM ontology). Is there somewhere a specification for this
format?
Best,
Hervé
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

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This message was sent using IMP, the Internet Messaging Program.
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

--
Geoff Barton Professor of Bioinformatics
Head of Division of Computational Biology College of Life Sciences
University of Dundee, Scotland, UK. g.j.barton@dundee.ac.uk
Tel:+44 1382 385860 www.compbio.dundee.ac.uk

The University of Dundee is registered Scottish charity: No.SC015096

5

Yes, under Tools->Preferences untick Open file at the bottom.

Geoff.

···

On 22/10/2013 17:21, Peter Felker wrote:

-- 
Geoff Barton                             Professor of Bioinformatics
Head of Division of Computational Biology   College of Life Sciences
University of Dundee, Scotland, UK.          [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk)
Tel:+44 1382 385860                         [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) 

The University of Dundee is registered Scottish charity: No.SC015096
6

Good afternoon Geoff
Our companies software is having issues with Jalview for the reason shown below.
do you have any suggestions how this can be resolved?

Thanks

PEter

···

Date: Tue, 22 Oct 2013 17:27:13 +0100
From: gjbarton@dundee.ac.uk
To: peter_felker@hotmail.com; jprocter@compbio.dundee.ac.uk; jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] question about the BLC format

Yes, under Tools->Preferences untick Open file at the bottom.

Geoff.

On 22/10/2013 17:21, Peter Felker wrote:

Good afternoon
I was wondering if there is a simple way to avoid the Jalview from showing a bunch of illustrative ways to use the data every time it starts up. These have to be closed before going to the real work.

Peter

Date: Tue, 22 Oct 2013 17:18:00 +0100
From: jprocter@compbio.dundee.ac.uk
To: jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] question about the BLC format

Hi Hervé.

The best documentation source is here:
http://www.compbio.dundee.ac.uk/manuals/scanps/subsection3_15_2.html

Jalview supports access to any of the iterations - when reading a BLC
file, you can put a ‘#’ after the filename to select
which iteration you want to import as an alignment. The BLC comment
section is imported and shown from the Alignment properties dialog.

Is that sufficient ? Or should we encourage Geoff to put up a more
detailed example :wink:

Jim.

Quoting “Hervé Ménager” hmenager@pasteur.fr:

Hi Jim & al.,
I’m looking for any kind of documentation regarding the BLC alignment
format which is supported by Jalview (I’m looking to register this
format in EDAM ontology). Is there somewhere a specification for this
format?
Best,
Hervé

Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

This message was sent using IMP, the Internet Messaging Program.

Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

_______________________________________________
Jalview-discuss mailing list
[Jalview-discuss@jalview.org](mailto:Jalview-discuss@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss)


-- 
Geoff Barton                             Professor of Bioinformatics
Head of Division of Computational Biology   College of Life Sciences
University of Dundee, Scotland, UK.          [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk)
Tel:+44 1382 385860                         [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) 

The University of Dundee is registered Scottish charity: No.SC015096

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