Jalview-Phyre2 Integration - Update & Change Requests

Jalview Developers
1

Hi Lawrence,

Hope this email meets you well.

We have made some progress with the Jalview-phyre2 integration. As you are aware, the following use cases were identified in the Jalview-Phyre2 collaboration document:

  1. Phyre2 users wanting to use Jalview
  2. Jalview users wanting to use Phyre2

I have pushed an initial prototype for the first use case to Jalview’s Phyre2 spike branch. A brief summary of the features enabled is outlined further below. There are some other features that would be best demonstrated. Accordingly, I think it is now time for us to have a look at it together via Skype when Jim is back (Jim is away this week and should be back on Monday). This will also enable us to obtain very useful feedback from you.

The current state of the implementation provides a good foundation for the second use case, which is yet to be implemented. I hope to commence implementation for Phyre2 Job submission and management from Jalview very soon. Once these are completed, it should plugin easily into the current implementation in such a way as to realise the second use case.

Furthermore, there are some changes required on Phyre2 server end, and I have summarised them under change request section below.

Features Enabled in the Current Prototype

  • Support for loading Phyre2 result alignment with custom Jalview annotation file generated by Phyre2
  • Detailed interactive sequence/structure display
  • Linking of the template sequences to their 3D structure models on importing the annotation file
  • Structure <–> Sequence mapping using the original fasta pair-wise alignment file generated by Phyre2
  • Superposing, viewing and comparing two or more modelled structured
  • Transfer of features and annotations from the modelled 3D structures onto their template sequence when viewed

Change Request

Changes to Phyre2 server

  1. The outset alignment file to be opened by the generated launchapp.jnlp Jalview file should be changed from “query.jal” to “allhits.fasta”
  2. For the sake of consistency, “query.jal.ann” should be rename to “allhits.jal.ann” since the “allhits.fasta” alignment file is made the outset input alignment.
  3. Drop custom mapping files specifically generated for Jalview (i.e “xxx.fasta.jal”)

Changes to the generated Jalview annotation file

  1. Modify the file accordingly to reference the original Phyre2 fasta mapping files generated rather than the custom ones stated in point three above
  2. Replace the name “QUERY” in STRUCTMODEL annotations with the actual name of the Query Sequence
  3. Make enhancement to the file to incorporate HEADER_STRUCT_MODEL annotation. See notes below:

HEADER_STRUCT_MODEL annotation:

  • The HEADER_STRUCT_MODEL annotation has been introduced to enable dynamic definition of the data columns for the STRUCTMODEL annotation.
  • The HEADER_STRUCT_MODEL should be tab-delimited just like STRUCTMODEL
  • The HEADER_STRUCT_MODEL should be declare once, and MUST be declared before the first instance of STRUCTMODEL
  • Each column of the HEADER_STRUCT_MODEL defines the corresponding columns in the STRUCTMODEL annotations
  • The first four columns of HEADER_STRUCT_MODEL (QUERY_SEQ, TEMPLATE_SEQ, MODEL_FILE, MAPPING_FILE) are compulsory and MUST be provided in the given order.
  • Data in STRUCT_MODEL can be formatted as HTML (as long as it contains no tab character)
  • Current implementation in Jalview enables backward compatibility - older “.jal.ann” annotation files generated by Phyre2 server can still be processed.
  • Infinite number of additional meta-data column can subsequently be included in any order. For instance the meta-data from the “crudlist" should be added to the annotation file as follows:

HEADER_STRUCT_MODEL QUERY_SEQ TEMPLATE_SEQ MODEL_FILE MAPPING_FILE Confidence % I.D Aligned Range Other Information
STRUCTMODEL FER_CAPAN c4n58A_ c4n58A_.1.pdb c4n58A_.1.fasta 1 54 48-143 PDB Header: Hyrolase
Chain: A
STRUCTMODEL FER_CAPAN d1a70a_ d1a70a_.2.pdb d1a70a_.2.fasta 1 71 48-144 Fold: Beta-Grasp (ubiquitin-like)

Please let me know if you find anything unclear regarding the requested changes. Apologies for the lengthy mail!

Best regards,
Charles

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

The University of Dundee is a registered Scottish Charity, No: SC015096

2

Hi Lawrence,

Thank you for the reply.

I think I am more concerned with having a consistent name for the query sequence across the essential artifacts processed by Jalview (allhits.fasta, pair-wise mapping fasta files and Jalview annotation file). I don’t mind if it is named “QUERY” or anything else - as far as it is persistent across board.

Currently, if a user submits a job to Phyre2 without providing a job description, the query sequence is named ‘undefined’ in the generated result artifacts (input.fasta, allhits.fasta, pair-wise mapping fasta files e.t.c). On the other hand, if a job description is provided, the query sequence is named using the provided description in the generated artifacts. Nonetheless, it is always named “QUERY" in the generated Jalview annotation file.

Do you foresee any challenge in naming the query sequence consistently across the artifacts?

Regards,
Charles

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

···

On Thu, Mar 30, 2017 at 11:47 AM, Charles Ofoegbu (Staff) <t.c.n.ofoegbu@dundee.ac.uk> wrote:

Hi Lawrence,

Hope this email meets you well.

We have made some progress with the Jalview-phyre2 integration. As you are aware, the following use cases were identified in the Jalview-Phyre2 collaboration document:

  1. Phyre2 users wanting to use Jalview
  2. Jalview users wanting to use Phyre2

I have pushed an initial prototype for the first use case to Jalview’s Phyre2 spike branch. A brief summary of the features enabled is outlined further below. There are some other features that would be best demonstrated. Accordingly, I think it is now time for us to have a look at it together via Skype when Jim is back (Jim is away this week and should be back on Monday). This will also enable us to obtain very useful feedback from you.

The current state of the implementation provides a good foundation for the second use case, which is yet to be implemented. I hope to commence implementation for Phyre2 Job submission and management from Jalview very soon. Once these are completed, it should plugin easily into the current implementation in such a way as to realise the second use case.

Furthermore, there are some changes required on Phyre2 server end, and I have summarised them under change request section below.

Features Enabled in the Current Prototype

  • Support for loading Phyre2 result alignment with custom Jalview annotation file generated by Phyre2
  • Detailed interactive sequence/structure display
  • Linking of the template sequences to their 3D structure models on importing the annotation file
  • Structure ↔ Sequence mapping using the original fasta pair-wise alignment file generated by Phyre2
  • Superposing, viewing and comparing two or more modelled structured
  • Transfer of features and annotations from the modelled 3D structures onto their template sequence when viewed

Change Request

Changes to Phyre2 server

  1. The outset alignment file to be opened by the generated launchapp.jnlp Jalview file should be changed from “query.jal” to “allhits.fasta”
  2. For the sake of consistency, “query.jal.ann” should be rename to “allhits.jal.ann” since the “allhits.fasta” alignment file is made the outset input alignment.
  3. Drop custom mapping files specifically generated for Jalview (i.e “xxx.fasta.jal”)

Changes to the generated Jalview annotation file

  1. Modify the file accordingly to reference the original Phyre2 fasta mapping files generated rather than the custom ones stated in point three above
  2. Replace the name “QUERY” in STRUCTMODEL annotations with the actual name of the Query Sequence
  3. Make enhancement to the file to incorporate HEADER_STRUCT_MODEL annotation. See notes below:

HEADER_STRUCT_MODEL annotation:

  • The HEADER_STRUCT_MODEL annotation has been introduced to enable dynamic definition of the data columns for the STRUCTMODEL annotation.
  • The HEADER_STRUCT_MODEL should be tab-delimited just like STRUCTMODEL
  • The HEADER_STRUCT_MODEL should be declare once, and MUST be declared before the first instance of STRUCTMODEL
  • Each column of the HEADER_STRUCT_MODEL defines the corresponding columns in the STRUCTMODEL annotations
  • The first four columns of HEADER_STRUCT_MODEL (QUERY_SEQ, TEMPLATE_SEQ, MODEL_FILE, MAPPING_FILE) are compulsory and MUST be provided in the given order.
  • Data in STRUCT_MODEL can be formatted as HTML (as long as it contains no tab character)
  • Current implementation in Jalview enables backward compatibility - older “.jal.ann” annotation files generated by Phyre2 server can still be processed.
  • Infinite number of additional meta-data column can subsequently be included in any order. For instance the meta-data from the “crudlist" should be added to the annotation file as follows:

HEADER_STRUCT_MODEL QUERY_SEQ TEMPLATE_SEQ MODEL_FILE MAPPING_FILE Confidence % I.D Aligned Range Other Information
STRUCTMODEL FER_CAPAN c4n58A_ c4n58A_.1.pdb c4n58A_.1.fasta 1 54 48-143 PDB Header: Hyrolase
Chain: A
STRUCTMODEL FER_CAPAN d1a70a_ d1a70a_.2.pdb d1a70a_.2.fasta 1 71 48-144 Fold: Beta-Grasp (ubiquitin-like)

Please let me know if you find anything unclear regarding the requested changes. Apologies for the lengthy mail!

Best regards,
Charles

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

The University of Dundee is a registered Scottish Charity, No: SC015096

–

Dr. Lawrence Kelley
Structural Bioinformatics Group
Dept. Life Sciences
Imperial College London
l.a.kelley@imperial.ac.uk
www.sbg.bio.ic.ac.uk/people/kelley

Phyre2 Lead Developer
www.imperial.ac.uk/phyre2

Twitter for server news
twitter.com/phyre2server

3

As I understand it, the query sequence is always first in the alignment (allhits, query.JAL and the template maps) Is that correct ?

If so, we could add logic to Jalview that defaults to adding annotation to the first sequence in the alignment if ‘QUERY’ is given as the name, but no sequence is given with that name.

Alternately, we have precedent for mapping annotation to sequences by position in the alignment. Much more fragile but equally valid in this case.

J.

···

On Thu, Mar 30, 2017 at 11:47 AM, Charles Ofoegbu (Staff) <t.c.n.ofoegbu@dundee.ac.uk> wrote:

Hi Lawrence,

Hope this email meets you well.

We have made some progress with the Jalview-phyre2 integration. As you are aware, the following use cases were identified in the Jalview-Phyre2 collaboration document:

  1. Phyre2 users wanting to use Jalview
  2. Jalview users wanting to use Phyre2

I have pushed an initial prototype for the first use case to Jalview’s Phyre2 spike branch. A brief summary of the features enabled is outlined further below. There are some other features that would be best demonstrated. Accordingly, I think it is now time for us to have a look at it together via Skype when Jim is back (Jim is away this week and should be back on Monday). This will also enable us to obtain very useful feedback from you.

The current state of the implementation provides a good foundation for the second use case, which is yet to be implemented. I hope to commence implementation for Phyre2 Job submission and management from Jalview very soon. Once these are completed, it should plugin easily into the current implementation in such a way as to realise the second use case.

Furthermore, there are some changes required on Phyre2 server end, and I have summarised them under change request section below.

Features Enabled in the Current Prototype

  • Support for loading Phyre2 result alignment with custom Jalview annotation file generated by Phyre2
  • Detailed interactive sequence/structure display
  • Linking of the template sequences to their 3D structure models on importing the annotation file
  • Structure ↔ Sequence mapping using the original fasta pair-wise alignment file generated by Phyre2
  • Superposing, viewing and comparing two or more modelled structured
  • Transfer of features and annotations from the modelled 3D structures onto their template sequence when viewed

Change Request

Changes to Phyre2 server

  1. The outset alignment file to be opened by the generated launchapp.jnlp Jalview file should be changed from “query.jal” to “allhits.fasta”
  2. For the sake of consistency, “query.jal.ann” should be rename to “allhits.jal.ann” since the “allhits.fasta” alignment file is made the outset input alignment.
  3. Drop custom mapping files specifically generated for Jalview (i.e “xxx.fasta.jal”)

Changes to the generated Jalview annotation file

  1. Modify the file accordingly to reference the original Phyre2 fasta mapping files generated rather than the custom ones stated in point three above
  2. Replace the name “QUERY” in STRUCTMODEL annotations with the actual name of the Query Sequence
  3. Make enhancement to the file to incorporate HEADER_STRUCT_MODEL annotation. See notes below:

HEADER_STRUCT_MODEL annotation:

  • The HEADER_STRUCT_MODEL annotation has been introduced to enable dynamic definition of the data columns for the STRUCTMODEL annotation.
  • The HEADER_STRUCT_MODEL should be tab-delimited just like STRUCTMODEL
  • The HEADER_STRUCT_MODEL should be declare once, and MUST be declared before the first instance of STRUCTMODEL
  • Each column of the HEADER_STRUCT_MODEL defines the corresponding columns in the STRUCTMODEL annotations
  • The first four columns of HEADER_STRUCT_MODEL (QUERY_SEQ, TEMPLATE_SEQ, MODEL_FILE, MAPPING_FILE) are compulsory and MUST be provided in the given order.
  • Data in STRUCT_MODEL can be formatted as HTML (as long as it contains no tab character)
  • Current implementation in Jalview enables backward compatibility - older “.jal.ann” annotation files generated by Phyre2 server can still be processed.
  • Infinite number of additional meta-data column can subsequently be included in any order. For instance the meta-data from the “crudlist" should be added to the annotation file as follows:

HEADER_STRUCT_MODEL QUERY_SEQ TEMPLATE_SEQ MODEL_FILE MAPPING_FILE Confidence % I.D Aligned Range Other Information
STRUCTMODEL FER_CAPAN c4n58A_ c4n58A_.1.pdb c4n58A_.1.fasta 1 54 48-143 PDB Header: Hyrolase
Chain: A
STRUCTMODEL FER_CAPAN d1a70a_ d1a70a_.2.pdb d1a70a_.2.fasta 1 71 48-144 Fold: Beta-Grasp (ubiquitin-like)

Please let me know if you find anything unclear regarding the requested changes. Apologies for the lengthy mail!

Best regards,
Charles

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

The University of Dundee is a registered Scottish Charity, No: SC015096

–

Dr. Lawrence Kelley
Structural Bioinformatics Group
Dept. Life Sciences
Imperial College London
l.a.kelley@imperial.ac.uk
www.sbg.bio.ic.ac.uk/people/kelley

Phyre2 Lead Developer
www.imperial.ac.uk/phyre2

Twitter for server news
twitter.com/phyre2server

4

Hi Jim,

As I understand it, the query sequence is always first in the alignment (allhits, query.JAL and the template maps) Is that correct ?

Yes that is indeed correct.

If so, we could add logic to Jalview that defaults to adding annotation to the first sequence in the alignment if ‘QUERY’ is given as the name, but no sequence is given with that name.

Alternately, we have precedent for mapping annotation to sequences by position in the alignment. Much more fragile but equally valid in this case.

We could certainly do so. However, doing so would defy the purpose of having the query sequence included in STRUCTMODEL annotation in the first place. Furthermore, given that we intend the implementation to be generic enough to support importation of modelled structures from other sources, I reckon that it would be more robust to explicitly define the relationships correctly rather than coding on assumptions.

Charles

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

···

On Thu, Mar 30, 2017 at 11:47 AM, Charles Ofoegbu (Staff) <t.c.n.ofoegbu@dundee.ac.uk> wrote:

Hi Lawrence,

Hope this email meets you well.

We have made some progress with the Jalview-phyre2 integration. As you are aware, the following use cases were identified in the Jalview-Phyre2 collaboration document:

  1. Phyre2 users wanting to use Jalview
  2. Jalview users wanting to use Phyre2

I have pushed an initial prototype for the first use case to Jalview’s Phyre2 spike branch. A brief summary of the features enabled is outlined further below. There are some other features that would be best demonstrated. Accordingly, I think it is now time for us to have a look at it together via Skype when Jim is back (Jim is away this week and should be back on Monday). This will also enable us to obtain very useful feedback from you.

The current state of the implementation provides a good foundation for the second use case, which is yet to be implemented. I hope to commence implementation for Phyre2 Job submission and management from Jalview very soon. Once these are completed, it should plugin easily into the current implementation in such a way as to realise the second use case.

Furthermore, there are some changes required on Phyre2 server end, and I have summarised them under change request section below.

Features Enabled in the Current Prototype

  • Support for loading Phyre2 result alignment with custom Jalview annotation file generated by Phyre2
  • Detailed interactive sequence/structure display
  • Linking of the template sequences to their 3D structure models on importing the annotation file
  • Structure ↔ Sequence mapping using the original fasta pair-wise alignment file generated by Phyre2
  • Superposing, viewing and comparing two or more modelled structured
  • Transfer of features and annotations from the modelled 3D structures onto their template sequence when viewed

Change Request

Changes to Phyre2 server

  1. The outset alignment file to be opened by the generated launchapp.jnlp Jalview file should be changed from “query.jal” to “allhits.fasta”
  2. For the sake of consistency, “query.jal.ann” should be rename to “allhits.jal.ann” since the “allhits.fasta” alignment file is made the outset input alignment.
  3. Drop custom mapping files specifically generated for Jalview (i.e “xxx.fasta.jal”)

Changes to the generated Jalview annotation file

  1. Modify the file accordingly to reference the original Phyre2 fasta mapping files generated rather than the custom ones stated in point three above
  2. Replace the name “QUERY” in STRUCTMODEL annotations with the actual name of the Query Sequence
  3. Make enhancement to the file to incorporate HEADER_STRUCT_MODEL annotation. See notes below:

HEADER_STRUCT_MODEL annotation:

  • The HEADER_STRUCT_MODEL annotation has been introduced to enable dynamic definition of the data columns for the STRUCTMODEL annotation.
  • The HEADER_STRUCT_MODEL should be tab-delimited just like STRUCTMODEL
  • The HEADER_STRUCT_MODEL should be declare once, and MUST be declared before the first instance of STRUCTMODEL
  • Each column of the HEADER_STRUCT_MODEL defines the corresponding columns in the STRUCTMODEL annotations
  • The first four columns of HEADER_STRUCT_MODEL (QUERY_SEQ, TEMPLATE_SEQ, MODEL_FILE, MAPPING_FILE) are compulsory and MUST be provided in the given order.
  • Data in STRUCT_MODEL can be formatted as HTML (as long as it contains no tab character)
  • Current implementation in Jalview enables backward compatibility - older “.jal.ann” annotation files generated by Phyre2 server can still be processed.
  • Infinite number of additional meta-data column can subsequently be included in any order. For instance the meta-data from the “crudlist" should be added to the annotation file as follows:

HEADER_STRUCT_MODEL QUERY_SEQ TEMPLATE_SEQ MODEL_FILE MAPPING_FILE Confidence % I.D Aligned Range Other Information
STRUCTMODEL FER_CAPAN c4n58A_ c4n58A_.1.pdb c4n58A_.1.fasta 1 54 48-143 PDB Header: Hyrolase
Chain: A
STRUCTMODEL FER_CAPAN d1a70a_ d1a70a_.2.pdb d1a70a_.2.fasta 1 71 48-144 Fold: Beta-Grasp (ubiquitin-like)

Please let me know if you find anything unclear regarding the requested changes. Apologies for the lengthy mail!

Best regards,
Charles

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

The University of Dundee is a registered Scottish Charity, No: SC015096

–

Dr. Lawrence Kelley
Structural Bioinformatics Group
Dept. Life Sciences
Imperial College London
l.a.kelley@imperial.ac.uk
www.sbg.bio.ic.ac.uk/people/kelley

Phyre2 Lead Developer
www.imperial.ac.uk/phyre2

Twitter for server news
twitter.com/phyre2server

5

Thanks for the reply, Charles.

As I understand it, the query sequence is always first in the
alignment (allhits, query.JAL and the template maps) Is that correct ?

Yes that is indeed correct.

Lawrence - is that also the case for all the alignments generated by the
phyre pipeline ?

If so, we could add logic to Jalview that defaults to adding
annotation to the first sequence in the alignment if 'QUERY' is given
as the name, but no sequence is given with that name.

Alternately, we have precedent for mapping annotation to sequences by
position in the alignment. Much more fragile but equally valid in this
case.

We could certainly do so. However, doing so would defy the purpose of
having the query sequence included in STRUCTMODEL annotation in the
first place.

Well in that case it could be made optional anyhow. Leaving it empty
means Jalview will assume the first sequence is the query (which is what
happens when processing other specialised prediction formats). The same
assumption could then be made when importing parwise mapping alignments
(where we already know what the template sequence ID is because it is
also given as a parameter).

Furthermore, given that we intend the implementation to be
generic enough to support importation of modelled structures from other
sources, I reckon that it would be more robust to explicitly define the
relationships correctly rather than coding on assumptions.

I take your point, but the asumption is only regarding the
interpretation of 'QUERY' which is a widely used generic label.

j.

ps. Thank goodness no one named a gene query!
http://www.ensembl.org/Multi/Search/Results?q=query;site=ensembl

···

On 04/04/2017 14:47, Charles Ofoegbu (Staff) wrote:

--
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk

6

Hi Jim,

I think it would be best if we could discuss these face to face when you are in tomorrow.

Charles

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

···

On 4 Apr 2017, at 17:09, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:

Thanks for the reply, Charles.

On 04/04/2017 14:47, Charles Ofoegbu (Staff) wrote:

As I understand it, the query sequence is always first in the
alignment (allhits, query.JAL and the template maps) Is that correct ?

Yes that is indeed correct.

Lawrence - is that also the case for all the alignments generated by the
phyre pipeline ?

If so, we could add logic to Jalview that defaults to adding
annotation to the first sequence in the alignment if ‘QUERY’ is given
as the name, but no sequence is given with that name.

Alternately, we have precedent for mapping annotation to sequences by
position in the alignment. Much more fragile but equally valid in this
case.

We could certainly do so. However, doing so would defy the purpose of
having the query sequence included in STRUCTMODEL annotation in the
first place.

Well in that case it could be made optional anyhow. Leaving it empty
means Jalview will assume the first sequence is the query (which is what
happens when processing other specialised prediction formats). The same
assumption could then be made when importing parwise mapping alignments
(where we already know what the template sequence ID is because it is
also given as a parameter).

Furthermore, given that we intend the implementation to be
generic enough to support importation of modelled structures from other
sources, I reckon that it would be more robust to explicitly define the
relationships correctly rather than coding on assumptions.

I take your point, but the asumption is only regarding the
interpretation of ‘QUERY’ which is a widely used generic label.

j.

ps. Thank goodness no one named a gene query!
http://www.ensembl.org/Multi/Search/Results?q=query;site=ensembl

–

Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk

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

The University of Dundee is a registered Scottish Charity, No: SC015096

7

Lawrence -

···

On 04/04/2017 17:30, Charles Ofoegbu (Staff) wrote:

I think it would be best if we could discuss these face to face when you
are in tomorrow.

Do you have some time tomorrow to be at the end of skype, google
hangouts or failing that, a plain old telephone ?

j.

8

Hi Lawrence,

I discussed this further with Jim this afternoon, we resolved that it would be better to name the query sequence as “QUERY” in the following generated artefacts: allhits.fasta, Jalview annotation, and pair-wise mapping files.

Consequently, custom pair-wise mapping file generation for Jalview should be retained, and then a custom allhits file with the query sequence named “QUERY” should be generated for Jalview.

Please let me know if you are ok with these.

Regards,
Charles

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

···

On 4 Apr 2017, at 17:30, Charles Ofoegbu (Staff) <t.c.n.ofoegbu@dundee.ac.uk> wrote:

Hi Jim,

I think it would be best if we could discuss these face to face when you are in tomorrow.

Charles

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

On 4 Apr 2017, at 17:09, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:

Thanks for the reply, Charles.

On 04/04/2017 14:47, Charles Ofoegbu (Staff) wrote:

As I understand it, the query sequence is always first in the
alignment (allhits, query.JAL and the template maps) Is that correct ?

Yes that is indeed correct.

Lawrence - is that also the case for all the alignments generated by the
phyre pipeline ?

If so, we could add logic to Jalview that defaults to adding
annotation to the first sequence in the alignment if ‘QUERY’ is given
as the name, but no sequence is given with that name.

Alternately, we have precedent for mapping annotation to sequences by
position in the alignment. Much more fragile but equally valid in this
case.

We could certainly do so. However, doing so would defy the purpose of
having the query sequence included in STRUCTMODEL annotation in the
first place.

Well in that case it could be made optional anyhow. Leaving it empty
means Jalview will assume the first sequence is the query (which is what
happens when processing other specialised prediction formats). The same
assumption could then be made when importing parwise mapping alignments
(where we already know what the template sequence ID is because it is
also given as a parameter).

Furthermore, given that we intend the implementation to be
generic enough to support importation of modelled structures from other
sources, I reckon that it would be more robust to explicitly define the
relationships correctly rather than coding on assumptions.

I take your point, but the asumption is only regarding the
interpretation of ‘QUERY’ which is a widely used generic label.

j.

ps. Thank goodness no one named a gene query!
http://www.ensembl.org/Multi/Search/Results?q=query;site=ensembl

–

Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk

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