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ncbi-epcr - Tool to test a DNA sequence for the presence of sequence tagged sites…  more info»

e-PCR.1.gz

E-PCR(1)                                                    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 ## 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
       <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 Pub‐
       lic License can be found in /usr/share/common-licenses/GPL.



                            February 2004                   E-PCR(1)
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