Dear all,
I have loaded a Uniprot alignment of 2 proteins in Jalview, everything worked perfect. However, I was not able to annotate a certain domain conserved in these 2 proteins (this is a standard domain detected by Uniprot). Is it possible to do it from the alignment file? If not is there another way around?
I would greatly appreciate recommendations!
Best regards,
Vera
Hello Vera,
If I understand your question, you have loaded alignment data from local files (e.g. Fasta) and would like to retrieve Uniprot annotation for these.
You can do this from Jalview menu option
Web Services | Fetch DB References | Standard Databases (or select Uniprot)
Note for this to work, your sequence ids should include a Uniprot identifier, e.g.:
FER_CAPAA
See section 4.2.1 of the Jalview Manual, at http://www.jalview.org/tutorial/TheJalviewTutorial.pdf, available on the documentation page http://www.jalview.org/about/documentation.
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK
www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017
From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Vera Belyaeva vera.belyaeva@ist.ac.at
Sent: 02 November 2017 21:07:00
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] sequence feature in Jalview
Dear all,
I have loaded a Uniprot alignment of 2 proteins in Jalview, everything worked perfect. However, I was not able to annotate a certain domain conserved in these 2 proteins (this is a standard domain detected by Uniprot). Is it possible to do it from the alignment file? If not is there another way around?
I would greatly appreciate recommendations!
Best regards,
Vera
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
The University of Dundee is a registered Scottish Charity, No: SC015096
That reply sent slightly prematurely!
I was going to write:
Note for this to work, your sequence ids should include a Uniprot identifier, e.g.:
FER_CAPAA
or
seq1|FER_CAPAA|pepper
Let us know if that helps!
Thanks,
Mungo
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK
www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017
From: Mungo Carstairs (Staff)
Sent: 03 November 2017 11:41:25
To: Vera Belyaeva; jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] sequence feature in Jalview
Hello Vera,
If I understand your question, you have loaded alignment data from local files (e.g. Fasta) and would like to retrieve Uniprot annotation for these.
You can do this from Jalview menu option
Web Services | Fetch DB References | Standard Databases (or select Uniprot)
Note for this to work, your sequence ids should include a Uniprot identifier, e.g.:
FER_CAPAA
See section 4.2.1 of the Jalview Manual, at http://www.jalview.org/tutorial/TheJalviewTutorial.pdf, available on the documentation page http://www.jalview.org/about/documentation.
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK
www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017
From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Vera Belyaeva vera.belyaeva@ist.ac.at
Sent: 02 November 2017 21:07:00
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] sequence feature in Jalview
Dear all,
I have loaded a Uniprot alignment of 2 proteins in Jalview, everything worked perfect. However, I was not able to annotate a certain domain conserved in these 2 proteins (this is a standard domain detected by Uniprot). Is it possible to do it from the alignment file? If not is there another way around?
I would greatly appreciate recommendations!
Best regards,
Vera
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
The University of Dundee is a registered Scottish Charity, No: SC015096