NAME

       ipcress - In-silico PCR experiment simulation system

SYNOPSIS

       ipcress [ options ] <primer file> <sequence paths>

DESCRIPTION

       ipcress is the In-silico PCR Experiment Simulation System.

       This  is  a  tool for simulation of PCR experiments.  You supply a file containing primers
       and a set of sequences, and it predicts PCR products.

       Ipcress is similar to the e-PCR program from the NCBI, but is much faster,  and  does  not
       suffer  from  problems  identifying  matches  when there are ambiguity symbols near primer
       ends.

       If you supply many primers pairs together, ipcress will simulate the  PCR  experiments  in
       parallel,  allowing  genome wide simulation of large numbers of experiments.  It uses many
       libraries from the exonerate sequence comparison tool.

INPUT FORMAT

       The input for ipcress is a simple white-space delimited file describing one experiment per
       line.  Each line contains the following 5 fields:

              id                An identifier for this experiment
              primer_A          Sequence for the first primer
              primer_B          Sequence for the second primer
              min_product_len   Minimum product length to report
              max_product_len   Maximum product length to report

       Here is an example line in this format:

       ID0001 CATGCATGCATGC CGATGCANGCATGCT 900 1100

OUTPUT FORMAT

       The  output  format  describes  one  PCR  product per-line, and is prefixed by "ipcress:",
       followed by the following 11 fields:

              sequence_id     The sequence identifier
              experiment_id   The PCR experiment id
              product_length  The PCR product length
              primer_5        The 5' primer (either A or B)
              pos_5           Position of the 5' primer
              mismatch_5      Number of mismatches on 5' primer
              primer_3        |
              pos_3           | Same fields for the 3' primer
              mismatch_3      |
              description     A description of the PCR product

       The description field is one of the following 4 strings:

              forward   Normal product, primer A followed by B
              revcomp   Normal product, primer B followed by A
              single_A  Bad product generated by primer_A only
              single_B  Bad product generated by primer_B only

       There is also a human-readable  output  displayed,  is  not  designed  for  parsing  (see:
       --pretty below).

GENERAL OPTIONS

       Most  arguments  have  short  and long forms.  The long forms are more likely to be stable
       over time, and hence should be used in scripts which call ipcress.

       -h | --shorthelp <boolean>
              Show help.  This will display a concise summary of the available options,  defaults
              and values currently set.

       --help <boolean>
              This  shows  all  the help options including the defaults, the value currently set,
              and the environment variable which may be used to set each parameter.   There  will
              be  an  indication  of  which  options  are  mandatory.   Mandatory options have no
              default, and must have a value supplied for ipcress to run.  If  mandatory  options
              are  used  in order, their flags may be skipped from the command line (see examples
              below).  Unlike this man page, the information from this option will always  be  up
              to date with the latest version of the program.

       -v | --version <boolean>
              Display the version number.  Also displays other information such as the build date
              and glib version used.

FILE INPUT OPTIONS

       -i | --input  <path>
              PCR experiment data in the ipcress file format described above.

       -s | --sequence <paths>
              Specify the sequences.  Multiple files may be specified here, which reduces the FSM
              building   overhead,  and  makes  ipcress  run  faster  than  running  the  process
              separately.

IPCRESS PARAMETERS

       -m | --mismatch  <mismatches>
              Specify the number of mismatches allowed per primer.  Allowing  mismatches  reduces
              the  speed  of the program as a large primer neighbourhood must be constructed, and
              fewer experiments can be fitted in memory  prior  to  each  scan  of  the  sequence
              databases.

       -M | --memory <Mb>
              Specify  the  amount  of  memory  the  program  should  use.   The more memory made
              available ipcress, the faster it will run, as more PCR experiments can be conducted
              in  each  scan of the sequence databases.  This does not include memory used during
              the scan (for storing partial results and  sequences),  so  the  actual  amount  of
              memory used will be slightly higher.

       -p | --pretty <boolean>
              Display results in a human-readable format, not designed for parsing.

       -P | --products <boolean>
              Display PCR products as a FASTA format sequence.

       -S | --seed <length>
              Specifiy  the  seed  length for the wordneighbourhood for the FSM.  If set to zero,
              the full primer is used.  Shorter words reduce the size of the  neighbourhood,  but
              increase the time taken by ipcress to filter false positive matches.

ENVIRONMENT

       Not documented yet.

EXAMPLES

       ipcress test.ipcress sequence.fasta
              This is the simplest way that ipcress can be used.
       ipcress dbsts_human.ipcress --sequence ncbi30/*.fasta --mismatch 1
              Compare  a  input  file against a set of fasta files, allowing one mismatch in each
              primer.

VERSION

       This documentation accompanies version 2.2.0 of the exonerate package.

AUTHOR

       Guy St.C. Slater.  <guy@ebi.ac.uk>.  See the AUTHORS file accompanying the source code for
       a list of contributors.

AVAILABILITY

       This source code for the exonerate package is available under the terms of the GNU general
       public licence.

       Please  see  the  file   COPYING   which   was   distrubuted   with   this   package,   or
       http://www.gnu.org/licenses/gpl.txt for details.

       This   package   has   been  developed  as  part  of  the  ensembl  project.   Please  see
       http://www.ensembl.org/ for more information.

SEE ALSO

       exonerate(1),e-PCR