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 ## discontiguos 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 alignmens (only if gaps>0), slow
a - Allways 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 ## discontinuos 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 alignmens (only if gaps>0), slow
a - Allways 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