Dear Noemi,
I’ll try to answer as much as I can below but others in the team should be able to add more details.
Firstly, you can retrieve sequences and align them directly within Jalview. You don’t need to get them from websites first, so steps 1-3 can all be done in Jalview. However, Jalview does not currently interface to NCBI but to EMBL-EBI which provides access to the same genomic data. For multiple alignment there are 8 tools under the webservices menu though not all support DNA/RNA.
If you have a gene loaded in jalview from Ensembl you can find its genomic start and end coordinates by right-clicking the ID for the sequence and selecting “Sequence details”. There is also a lot of other information present there too. This information is overlaid on the sequence as sequence “Features” that you can customise (see View->Feature Settings). Feature settings for DNA/RNA don’t currently include everything, but near-future versions of Jalview will have more there that can also be carried across to the protein alignment view.
Jalview 2.11 supports VCF files so most variants can be added if they are in that format. However, this is a new feature in Jalview and we are still actively developing it, so if it does not do what you need or it is not clear how to do selections from the VCF then let us know.
If Jalview’s current built-in functions don’t quite overlay what you want to do you can create your own “feature file” to add features to a sequence, or an “annotation file” to add annotations under an alignment. The documentaiton explains how to do this. Once you have the file, you just drag and drop it onto your alignment.
Remember as well that you can always save your Jalview session and go back to it later or pass it on to someone else to look at. (File->Save Project).
Also, to learn more about Jalview please try the YouTube videos that Dr Suzanne Duce has developed. These cover most of the key Jalview functions and features in nice 4 min tutorials. If there is anything missing there, let us know.
Finally, my group has a strong research interest in the analysis of variants and this is one reason why we have put a lot of effort into supporting DNA/RNA and variants in Jalview. However, we support Jalview for all, and there are many ways in which variant data might be used in different contexts so we are also keen to hear your suggestions and use-cases for these features.
I hope this helps,
Geoff.
P.S. we are working on the problem with subscribing to jalview-discuss. Hopefully there will be a fix soon!
Dear Professor Barton,
Thank you so much for your response.
My end goal is to use the alignment information to design SMN1-specific PCR primers (avoiding those genomic locations with identity to SMN2 pseudogene). To accomplish that, I need to find the genomic coordinates of those locations unique to SMN1. In addition, I’d like to overlay that information with ClinVar and HGMD variants to avoid designing primers over locations with SNPs or variants.
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I downloaded the FASTA file for gene and pseudogene from NCBI
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I aligned both sequences using kalign (clustalw output)
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I uploaded the alignment in Jalview
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I selected File>Fetch Sequences>ENSEMBL (SMN1 ID: ENSG00000172062)
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I selected Web Service> Fetch DB References to obtain genomic coordinates, but I wasn’t able to retrieve the genomic coordinates. What am I missing?
Can ClinVar or HGMD variants track be imported into Jalview?
I guess I am trying to figure out a tool that can display all the information (alignment, genomic coordinates, ClinVar, HGMD variants). Not sure if Jalview is the tool, but it certainly looks capable of doing that, I am just new at it.
Thanks again,
Noemi
From: Geoff Barton [mailto:gjbarton@dundee.ac.uk]
Sent: Thursday, October 31, 2019 8:13 AM
To: Vidal Folch, Noemi; Jalview-discuss@jalview.org; help@jalview.org
Subject: [EXTERNAL] Re: Jalview Fetch Sequences
Dear Noemi,
Thanks for your email.
Sorry that you have not been able to subscribe to Jalview-discuss ! There have been some major changes to our University network over recent months and this is one of several problems that were not noticed. Thank you for letting us know.
With regard to your question:
- If you load your DNA sequences from Ensembl (Fetch Sequences->Ensembl) then once you have loaded your sequences you can cross-reference to the corresponding protein sequences by going to calculate->Get cross-references->Uniprot. This should bring up a split-view with DNA/RNA in the top window and Protein in the lower.
The default view for Genomic DNA is to “hide” the introns in the display, but you can reveal these parts of the sequence either under the “View” menu or by clicking on the little blue triangles above the alignment with the right mouse button to reveal specific introns.
- You don’t say where your sequences have come from, but if they have IDs that include the genomic coordinates and database then you “might” be able to “discover” other information about the sequences by going to Web Service->Fetch DB References.
I hope this helps, but if you have further questions please write again to help@jalview.org Once we have the mailing list subscription working properly again that will be the best way to ask since it reaches more people who might be able to help.
I’ve copied your email and this answer to the mailing list as well since others might be interested in the answer. Also, others in the Jalview team might comment if I have left things out!
All the best,
Geoff.
Hello,
My name is Noemi Vidal-Folch. I work as a scientist at Mayo Clinic. I am interested in using Jalview, but having difficulties with fetching sequences. I tried subscribing to the Jalview Discussion List but unfortunately I received a message that “You don’t have permission to access /mailman/subscribe/jalview-discuss on this server”.
I have loaded the DNA sequence alignments for a gene and its pseudogene. I would like to overlay the reference sequence with genomic coordinates. Which import/fetch function should I use? Could someone provide a resource for help? I have not been able to find the answer in either the video tutorials, FAQ or the documentation manual.
Thank you in advance,
Noemi Vidal-Folch
Development Technologist
Biochemical Genetics Laboratory
Department of Laboratory and Medicine Pathology
Phone: 507-538-0314
E-mail: vidalfolch.noemi@mayo.edu
Mayo Clinic
200 First Street S.W.
Rochester, MN 55905
www.mayoclinic.org
--
Geoff Barton, FRSE FRSB | Professor of Bioinformatics | Head of Division of Computational Biology
School 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) | twitter: @gjbarton
The University of Dundee is registered Scottish charity: No.SC015096
The University of Dundee is a registered Scottish Charity, No: SC015096
The University of Dundee is a registered Scottish Charity, No: SC015096
···
On 31/10/2019 17:17, Vidal Folch, Noemi wrote:
--
Geoff Barton, FRSE FRSB | Professor of Bioinformatics | Head of Division of Computational Biology
School 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) | twitter: @gjbarton
The University of Dundee is registered Scottish charity: No.SC015096