update May  25, 2009
NAME

blrevcomp - create reverse, complement, or reverse-complement strands

SYNOPSIS
blrevcomp  [-r | -c | -f]  infile  outfile
java -jar blrevcomp.jar  [options] infile  outfile
DESCRIPTION
blrevcomp reads a file containing one or more DNA or RNA sequences in either FASTA or GDE flat file format and creates the reverse complement, the complement, or reverse strand. In Fasta files, sequence names begin with '>', and in GDE flat files, sequence names begin with '#'.  The sequences may contain any of the standard IUPAC ambiguity characters as defined in Cornish-Bowden (1985) Nucl. Acids Res. 13:3021-3030. If gap characters ('-') are present in a sequence, they are retained in the output. If 'U' or 'u' are detected in a sequence, it is assumed to be RNA. Otherwise, it is assumed to be DNA.

OPTIONS

-r (default) - reverse and complement
-c - complement only. If the input strand is 5'-->3', the output strand is 3' --> 5'
-f  - reverse only (flip). If the input strand is 5'-->3', the output strand is 3' --> 5'


TODO
1. There should probably be a way to have this program know whether an input sequence is circular or linear, and return that information.
AUTHOR
Dr. Brian Fristensky
Department of Plant Science
University of Manitoba
Winnipeg, MB  Canada R3T 2N2
frist@cc.umanitoba.ca
http://home.cc.umanitoba.ca/~frist