Hi Dimitris -
The best place to ask for Jalview help is the Jalview discussion list: sign up at http://www.jalview.org/mailman/listinfo/jalview-discuss
I’ve cced the list with my reply so others can benefit!
Hope you are all well. Prompted to contact you with my questions about Jalview from Edinburgh Genomics Admin. So here it goes. if i have a fasta file with nucleodite alignment sequences (that i got from contra v3), can i upload them in your program in order to see sequencing/coordinates conservation between diverse species?
Jalview will read a FASTA file - if they have been aligned by Contra then you can see conserved nucleotides straight away using the ‘PID’ coloursheme and via the ‘Consensus’ annotation row.
Do i need to convert the alignment ,once its loaded into jailview, to amino acid alignment in order for me to see conservation?
It depends on your needs. If you are only interested in transcription factor binding sites then conservation will be evident at the nucleotide level.
Also how do I convert a DNA sequence to amino acid sequence? (And vise versa) I can’t seem to find it.
You can translate nucleotide sequences to proteins via the Calculate menu’s ‘Translate CDNA’ submenu - which provides a range of different translation tables. Jalview doesn’t provide backtranslation - but if you do have CDS sequences for proteins, you can have Jalview reconstruct a nucleotide alignment.
See Jalview’s built in help http://www.jalview.org/help/html/features/splitView.html#opensplit
(i got a question about contra v3 as well but dont know if you know the answer so i will ask it anyway, once you get the zip file with your results. It produces fasta files as blocks1,2,3,etc but also a larger fasta file but that fasta file doesnt contain all the blocks together, i would like to add all this blocks together so i could do that analysis into jalview, any idea how?)
Jalview doesn’t have a ‘Concatenate alignments’ option as yet. There are a few ways you could do this (e.g. export all three block alignments as BLC format into text windows, and copy and paste the alignment data from blocks two and three onto the first). Take a look at video 5 (https://youtu.be/xT4gKV6F_Vk) from the training videos page (http://www.jalview.org/training/Training-Videos) to learn about this.
Hope this helps you get going - we covered much of what you asked in our edinburgh genomics training course… which we’ll be running again later this year. Keep an eye out on our web site for the announcement !
Jim.
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On 07/05/2020 10:22, Dimitris Hatzopoulos wrote:
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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](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)