NAME
ipcress - In-silico PCR experiment simulation systemSYNOPSIS
ipcress [ options ] <primer file> <sequence paths>DESCRIPTION
ipcress is the In-silico PCR Experiment Simulation System.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
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
- 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
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.fastaThis 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. <[email protected]>. 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.SEE ALSO
exonerate(1),e-PCRMarch 2003 | ipcress |