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 <[email protected]> and Andreas Tille <[email protected]> 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.