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.

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.