perlprimer(1) [debian man page]

PERLPRIMER(1)						      General Commands Manual						     PERLPRIMER(1)

NAME

       perlprimer - graphically specify amplicon of DNA or mRNA sequences and design primers

SYNOPSIS

       perlprimer

DESCRIPTION

       PerlPrimer  calculates primer melting temperature using J. SantaLucia's extensive nearest-neighbour thermodynamic parameters. To adjust for
       the salt conditions of the PCR, PerlPrimer uses the empirical formula derived by von Ahsen, et al. (2001) and allows the  user  to  specify
       the  concentration of Mg2+, dNTPs and primers, or use standard PCR conditions. The result is a highly accurate prediction of primer melting
       temperature, giving rise to a maximum yeild of product when amplified.	PerlPrimer is written in Perl and requires Perl/Tk.  In  addition,
       for  QPCR  functionality PerlPrimer requires the open-source Spidey executable from NCBI. The program is designed to be cross-platform com-
       patible and has been developed and tested on both Microsoft Windows and GNU/Linux-based operating systems. Users have also reported success
       using the program under Mac OS X.

SEE ALSO

	A very nice tutorial on http://perlprimer.sourceforge.net is also distributed as a debian package perlprimer-doc.

AUTHOR

       perlprimer was written by Owen Marshall <owenjm@users.sourceforge.net>

       This manual page was assembled by Steffen Moeller <steffen_moeller@gmx.de>, for the Debian project (but may be used by others).

								  6 January 2005						     PERLPRIMER(1)

RE-PCR(1)						      General Commands Manual							 RE-PCR(1)

NAME

       re-PCR -- Find sequence tagged sites (STS) in DNA sequences

SYNOPSIS

       re-PCR [-hV] -p hash-file [-g gaps] [-n mism] [-lq] [primer ...]

       re-PCR [-hV] -P hash-file [-g gaps] [-n mism] [-l] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [primers-file ...]

       re-PCR [-hV] -s hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-o outfile] [-r+|-] [left right lo[-hi] [...]]

       re-PCR [-hV] -S hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [stsfile ...]

DESCRIPTION

       Implements reverse searching (called Reverse e-PCR) to make it feasible to search the human genome sequence and other large genomes by per-
       forming STS and primer searches.

OPTIONS

       -p=hash-file
		 Perform primer lookup using hash-file

       -P=hash-file
		 Perform primer lookup using hash-file

       -s=hash-file
		 Perform STS lookup using hash-file

       -S=hash-file
		 Perform STS lookup using hash-file

       -n=mism	 Set max allowed mismatches per primer for lookup

       -g=gaps	 Set max allowed indels per primer for lookup

       -m=margin Set variability for STS size for lookup

       -l	 Use presize alignments (only if gaps>0)

       -G	 Print alignments in comments

       -d=min-max
		 Set default STS size

       -r=+|-	 Enable/disable reverse STS lookup

       -O=+|-	 Enable/disable syscall optimisation

       -C=batchcnt
		 Set number of STSes per batch

       -o=outfile
		 Set output file name

       -q	 Quiet (no progress indicator)

EXAMPLE

	famap -tN -b genome.famap org/chr_*.fa

	fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap

	re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200

       See famap(1) and fahash(1)

SEE ALSO

       /usr/share/doc/ncbi-epcr/README.txt

       bioperl(1), e-pcr(1), famap(1) and fahash(1)

AUTHORS

       This manual page was written by 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.

								    April 2008								 RE-PCR(1)