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: 1. 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. 2. 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 [email protected]<mailto:[email protected]> 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. On 30/10/2019 21:14, Vidal Folch, Noemi wrote: 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: [email protected]<mailto:[email protected]> ________________________________________ Mayo Clinic 200 First Street S.W. Rochester, MN 55905 www.mayoclinic.org<http://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 | [email protected]<mailto:[email protected]> 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
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