[EMBOSS] showalign: maintain numbering of the reference sequence

[Ingo P. Korndoerfer]

dear fellow emboss users,

who can help me out with this one:

we URGENTLY need some commandline driven program, that nicely displays
emma output, BUT MAINTAINS the sequence numbering of the reference sequence.

showalign seems to simply start counting at the first residue, even if
it is a construct with just a purification tag, and happily includes
alignment gaps in the numbering.

this makes it real difficult for us to find a certain residue of a
protein in our alignment, particularly important if the whole team wants
to discuss certain details ...

i have tried the refseq keyword, but that did not seem to do that ...

any ideas, i'd be happy. would be nice if it were in emboss, since that
is installed on all machines already, but if need to, we can install
additional software ...

greetings

ingo

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