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================================================================
Electronic PCR (e-PCR) program for finding STSs in DNA sequences
================================================================
REFERENCE: G.D.Schuler. Sequence mapping by Electronic PCR.
Genome Research 7: 541-550, 1997.
FEEDBACK: schuler@ncbi.nlm.nih.gov
USAGE: e-PCR <stsfile> <seqfile>
Where <stsfile> is one of the files in the db directory or
one that you supply (see below for format specification)
and <seqfile> is a FASTA-style file containing any number
of sequences.
SYSTEMS SUPPORTED
=================
Sun Solaris 5.9/Sparc
Sun Solaris 5.9/x86
Linux/i386 (glibc-2.2.4)
INSTALLATION
============
Just identify the correct executable for your system and copy to a
location that is on the search path. You can use any of the following
commands to test the program; they should all produce some output.
e-PCR db/genethon.sts samples/L78833.nt
e-PCR db/genethon.sts samples/U47924.nt
e-PCR db/txmap.sts samples/U47924.nt
STS DATABASE FILES
==================
genethon.sts Genethon genetic markers (Dib et al, 1996)
txmap.sts Transcript Map markers (Schuler et al, 1996)
STS DATABASE FILE SPECIFICATION
===============================
The stsfile should contain at least four (optionally five)
tab-delimited columns:
col-1: STS name
col-2: left PCR primer
col-3: right PCR primer
col-4: PCR product size
col-5: (optional) additional text to be included in the output
PACKING LIST
============
./README
./bin/sunos-sparc/e-PCR
./bin/sunos-intel/e-PCR
./bin/linux-intel/e-PCR
./db/dbsts.sts
./db/genethon.sts
./db/txmap.sts
./samples/L78833.nt
./samples/U47924.nt
./src/e-PCR.cpp
./src/fasta-io.cpp
./src/fasta-io.h
./src/Makefile
./src/stsmatch.cpp
./src/stsmatch.h
./src/util.cpp
./src/util.h
./src/gdsutil.cpp
./src/gdsutil.h
./src/version.h
THANKS
======
Serge Batalov
|
