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e-PCR

Langue: en

Version: 265317 (debian - 07/07/09)

Section: 1 (Commandes utilisateur)

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.

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