Reverse Complement utility

Keith James k.james at bangor.ac.uk
Tue Aug 5 08:39:39 EST 1997


magoldst at ix.netcom.com (Marc Goldstein) writes:

> 
> Hi,
> 
> I am looking for a very simple utility that can run in the Win95 
> environment that will take an input sequence of up to a KB and create the 
> reverse-complement of it, and save that. The input could be either ascii 
> or GCG or similar or even just copy-paste into the utility.
> 
> Anyone know of a utility to accomplish this? Please remove NOSPAM in 
> my address if using auto-reply functions.

Ignore this if you don't have Unix (or Windows + win32-Perl + Cygwin32 GNU
fileutils). If you have Perl available you can do:

perl -ln0e 'tr/ACGTNacgtn- /TGCANtgcan/d; print scalar reverse $_;' <infile

This will remove any "-" and spaces, though. To write to a file instead
of the screen, just add >outfile to the end, of course. Only for ascii
files... you will get a horrible mess with a GCG file! It's a handful to
type, so I alias it to something short. If you use GNU csplit you can get
it to take Pearson/Fasta files by splitting on the headers and directing
the output files through this.

-- 
Keith James Ph.D. - k.james at bangor.ac.uk  PGP 2.6.2i  Key ID 469A9FA1
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