Hi Kim and everyone
I would echo Carton's idea that it would be good to have a way to colour each CDS to reflect GC3, but I would extend it further because there are potentially other quantitative values that one could associate with genes and display visually in Artemis. What about gene expression data, for example? Or Blast scores? Of course, these cannot be calculated from the sequence (unlike GC3), so would need the user to provide a file with values for each feature that Artemis would then translate into colours and display.
Actually, I think it should already be possible to do this, because Artemis understands a "/colour=R G B" qualifier. So if Carton writes a script to calculate GC3, convert this into RGB colour values and insert the appropriate /colour qualifier for each CDS into the file, he can see his genes in glorious colour. It would be nice if the Artemis people made it easier, though!
On a related note, we would like to be able to use different colours in the comparison window of ACT. As well as the current red and pinks for the lines connecting matches, we would like to use other colours to show different classes of match (in our case, genes supporting different phylogenies, but it could be functional classes, or whatever). How about allowing multiple comparison files to be loaded, with the user choosing the colour for each?
Peter
Kim Rutherford wrote:
Hi Carton.
On Mon, 23 Aug 2004 21:15:41 +0800, Carton Chen wrote:
Dear Kim,
I saw the new version of Artemis. I downloaded it, add the ,command suffix and test ran it a little bit. I like it. It is significantly faster. more responsive, and more convenient.
A thought occurred to me recently regarding Artemis. It would be great if you let the ORF arrows show info regarding their codon preferences in color: Different colors (say from Red to orange to yellow to green to blue to cyan) for different range (100 to 0%) of G/C in the third position of codon, This way one may look at the ORF and readily decide which one is likely coding in G+C rich or G+C poor genomes.
That's an interesting suggestion. I'm CCing this to the Artemis mailing list so others can comment.
Another alternative of course is to give the ORF the same color that matches the corresponding curve in the CC Frame Plot. That would be very helpful, too.
That sort of thing has been discussed in the past, but it never made it to the top of the priority list.
Another suggestion:
At least in prokaryote mode (if there is), the initial ORF mapped should start with the first potential initiation codon after the last stop codon, not just the first codon after. The latter adds a lot extra work - at least one initial move for each potential ORF.
I'm sure there is reason for this behaviour. I'll leave it to others to comment.
Kim.
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