Re: is something wrong in it?


Rita wrote:
> >
> > If "mfold" is Zuker's RNA secondary structure prediction script, then
> > (according to the online doc at
> > http://www.bioinfo.rpi.edu/~zukerm/seqanal/node3.html) the command usage is
> >
> > mfold SEQ=`file_name' with optional parameters:
> > [ AUX=`auxfile_name' ] [ RUN_TYPE=text (default) or html ]
> > [ NA=RNA (default) or DNA ] [ LC=sequence type (default = linear) ]
> > [ T=temperature (default = 37°) ] [ P=percent (default = 5) ]
> > [ W=window parameter (default - set by sequence length) ]
> > [ MAXBP=max base pair distance (default - no limit) ]
> > [ MAX=maximum number of foldings to be computed (default 100) ]
> > [ ANN=structure annotation (default = none, p-num or ss-count) ]
> > [ START=5' base # (default = 1)] [ STOP=3' base # (default = end) ]
> > [ REUSE=NO/YES (default=NO) reuse existing .sav file ]
> >
> > It looks like, at a minimum, you have to enter
> > ./mfold SEQ=/your/file/name/goes/here
> > substituting the name of your RNA sequence file for
> > /your/file/name/goes/here
>
> Exactly. I am doing this same thing but first I have ti write ./mfold
> place of mfold.
> Second It doesnot work at home ,I have to change directory.
> and third thing is after all this this command also not working it is
> giving me "mfold version 3.2 " in some structure shape .
> and than REUSE= NO
> ./mfold: line 1: reformat-seq.sh: command not found
> auxgen failed
> job aborted
> Can you tell me why?
> Thanks


Please If you are familier with mfold server ,Help me.
I am trying to run this thing from last 4 days but it is not working.
Thanks.

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