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ipcress(1) PCR simulation tool ipcress(1) 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 con- taining 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 ambi- guity 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 compar- ison 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 pars- ing (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 op- tions, 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 or- der, 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 mis- matches reduces the speed of the program as a large primer neigh- bourhood 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 mem- ory made available ipcress, the faster it will run, as more PCR ex- periments can be conducted in each scan of the sequence databases. This does not include memory used during the scan (for storing par- tial 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 pars- ing. -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 fil- ter 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 mis- match 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 ipcress March 2003 ipcress(1)
NAME | SYNOPSIS | DESCRIPTION | INPUT FORMAT | OUTPUT FORMAT | GENERAL OPTIONS | FILE INPUT OPTIONS | IPCRESS PARAMETERS | ENVIRONMENT | EXAMPLES | VERSION | AUTHOR | AVAILABILITY | SEE ALSO
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