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 ## 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
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.