seqed?

[Peter Rice]

Daniel Schlieper wrote:
> 
> thank you very much. Yes mse is a bit hidden, but Peter Rice was as kind
> as to point me to that. In total, mse seems to be much better than seqed,
> and I will be happy to use it.
> 
> Just in case if there is anybody interested in even improving it, there
> might two minor improvments possible:
> 
> 1. There could be a check feature as in seqed. For example (from seqed):
> 
>      aacgggttaaggcct
>         ^      ^^^^
>      aaccggttaaccggt
> ....|.........|.........|....
>     0        10        20


Aaaahhhhh .... that is rather nasty to implement.

In SEQED it was really there for people typing in data from sequencing
gels, and in particular for the "digitizer" input (a digitizer was a table
with a pen where you clicked the pen tip on the 4 corners, on the lanes,
and then on each band). The check mode was to compare two runs in order to
catch clicks that were in between bands.

Far simpler is to simply enter the sequence twice, then use wordmatch to
compare them (again, that is basically what I used to do with SEQED
anyway).

> 2. There could be a way to read an empty (or not yet existing file). Now
> it says:
> 
> Unix % mse i.seq
> Multiple Sequence Editor
> Error: failed to open filename i.seq
> Error: Unable to read sequence 'i.seq'

That one is a simple EMBOSS global change, allowing an input "sequence set"
to be empty. Basically, adding the nullok attribute for sequences, or
perhaps a minimum number of sequences for a sequence set (default 1, emma
would like more, mse could handle 0). Expect something in a future release.

Peter

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723