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EMBOSS FAQ (Frequently Asked Questions)
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Q) Is there a maximum size for sequences?
A) The maximum size for any program depends only on how much memory your
system has.
Of course, some programs (and some program options) can take up too
much memory, or simply run very slowly.
You might have a constraint imposed on your usage of memory.
Try using the Unix command 'limit' to look at such constraints.
Try using the Unix command 'unlimit' to remove the constraints, eg:
% unlimit stacksize
% unlimit vmemoryuse
Q) GCG has a somewhat arbitrary fragment length limit of 2500 bp for gel*.
Is there a similar limit for MSE under EMBOSS?
A) No. MSE has no limit, you are only limited by how much memory you
have.
Q) I am trying to write a web interface for an emboss program
and run apache. The program complains that there is no HOME
directory set.
A) Just put these at the top after your 'use CGI' ( whatever) statements.
$ENV{HOME}= i.e. /usr/local/apache
$ENV{EMBOSS_DATA}=
These two are important, but you can also pass other "constants".
Q) Plotting with pepwheel gives interesting output.
pepwheel -turns=8 -send=30 sw:p77837 -auto
gives a helical wheel plot but the residues are plotted so every two
circles are sat on top of one another.
A) That is the correct answer.
Instead of 3.6 residues per turn, (5 turns in 18 steps) you seem to
have a helix with 8 turns in 18 steps (4 in 9).
Try -turns=4 -steps=9 ... but only if you are sure that is the
way your helix goes.
I suppose we could play with checking for common factors in pepwheel,
but I don't know of any biologically meaningful setting that would
cause problems.
Q) In prettyplot, How do you specify an output file name for the plot file?
A)
prettyplot -auto ~/wordtest/globin-nogap.msf -graph ps
Created prettyplot.ps
The name is generated automatically. To set this to something more
discriptive use -go .i.e
prettyplot -auto ~/wordtest/globin-nogap.msf -graph ps -go=hello
Created hello.ps
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