Ok, so one more thing while I am at it. Searching with regexes is fine and powerful with protein sequences but when dealing with nucleotide sequences the IUPAC codes are the only reasonable way to go in my opinion. Would it be possible to have IUPAC as a checkbox in the find dialogue? As far as I can see, jalview does not know whether it is analysing nucleotides or aa so automating this would be a larger undertaking, but a checkbox which remembers its state would be just excellent
Ok, enough for now...
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Ok, so one more thing while I am at it. Searching with regexes is fine and powerful with protein sequences but when dealing with nucleotide sequences the IUPAC codes are the only reasonable way to go in my opinion. Would it be possible to have IUPAC as a checkbox in the find dialogue? As far as I can see, jalview does not know whether it is analysing nucleotides or aa so automating this would be a larger undertaking, but a checkbox which remembers its state would be just excellent
All possible in principle, and it would certainly be useful for those
who don't live and breath regex. We'll see what the next Jalview
post-doc says when they take up their position.
Regexes are excellent in many situations, but as it is; many other software uses the iupac one-letter code and cutting and pasting sequences gets cumbersome. In the meantime I could write a script to translate the pasted seq to jalview on-the-fly, which would be an ok workaround.
I'll add yet another suggestion connected to the iupac symbols and that would be to have the option of using these for the nucleotide consensus row.
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···
On 29-01-2008 at 15:20, James Procter <jimp@compbio.dundee.ac.uk> wrote:
Jonas Larsson wrote:
Ok, so one more thing while I am at it. Searching with regexes is fine and
powerful with protein sequences but when dealing with nucleotide sequences
the IUPAC codes are the only reasonable way to go in my opinion. Would it be
possible to have IUPAC as a checkbox in the find dialogue? As far as I can
see, jalview does not know whether it is analysing nucleotides or aa so
automating this would be a larger undertaking, but a checkbox which remembers
its state would be just excellent
All possible in principle, and it would certainly be useful for those
who don't live and breath regex. We'll see what the next Jalview
post-doc says when they take up their position.
