E-PCR(1)						      General Commands Manual							  E-PCR(1)

NAME

       e-PCR -- Find sequence tagged sites (STS) in DNA sequences

SYNOPSIS

       e-PCR [-hV] [posix-options] stsfile [fasta ...] [compat-options]

DESCRIPTION

       The program substitutes blast in the location of pairs primers on the genome that may yield a PCR product.

OPTIONS

       posix-options are:

       -m=##	 Margin (default 50)

       -w=##	 Wordsize  (default 7)

       -n=##	 Max mismatches allowed (default 0)

       -g=##	 Max indels allowed (default 0)

       -f=##	 Use ## disontiguous words, slow if ##>1

       -o=##	 Set output file

       -t=##	 Set output format:

		 1 - classic, range (pos1..pos2)

		 2 - classic, midpoint

		 3 - tabular

		 4 - tabular with alignment in comments (slow)

       -d=##-##  Set default size range (default 100-350)

       -p=+-	 Turn hits postprocess on/off

       -v=##	 Verbosity flags

       -a=a|f	 Use presize alignments (only if gaps>0), slow

		 a - Always or f - as Fallback

       -x=+-	 Use 5'-end lowercase masking of primers (default -)

       -u=+-	 Uppercase all primers (default -)

       compat-options (duplicate posix-options) are

       M=##	 Margin (default 50)

       W=##	 Wordsize  (default 7)

       N=##	 Number of mismatches allowed (default 0)

       G=##	 Max indels allowed (default 0)

       F=##	 Use ## discontinuous words

       O=##	 Set output file to ##

       T=##	 Set output format (1..3)

       D=##-##	 Set default size range

       P=+-	 Postprocess hits on/off

       V=##	 Verbosity flags

       A=a|f	 Use presize alignments (only if gaps>0), slow

		 a - Always or f - as Fallback

       X=+-	 Use 5'-end lowercase masking of primers (default -)

       U=+-	 Uppercase all primers (default -)

       -mid	 Same as T=2

       For information about further options just call e-PCR without any options.

SEE ALSO

       /usr/share/doc/ncbi-epcr/README.txt

       bioperl(1), re-pcr(1)

AUTHORS

       This manual page was written by Steffen Moeller <moeller@debian.org> and Andreas Tille <tille@debian.org> for the Debian system (but may be
       used by others).  Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public  License,
       Version 2 any later version published by the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

								   February 2004							  E-PCR(1)