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Digestor

Generic Workflow Nodes for KNIME: OpenMS version 2.6.0.202009301213 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Digests a protein database in-silico.

Web Documentation for Digestor

Options

version
Version of the tool that generated this parameters file.
missed_cleavages
The number of allowed missed cleavages
min_length
Minimum length of peptide
max_length
Maximum length of peptide
enzyme
The type of digestion enzyme
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overrides tool-specific checks
test
Enables the test mode (needed for internal use only)
ID
Identifier to use for each peptide: copy from parent protein (parent); a consecutive number (number); parent ID + consecutive number (both)
description
Keep or remove the (possibly lengthy) FASTA header description. Keeping it can increase resulting FASTA file significantly.

Input Ports

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input file [fasta]

Output Ports

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Output file (peptides) [idXML,fasta]

Views

Digestor Std Output
The text sent to standard out during the execution of Digestor.
Digestor Error Output
The text sent to standard error during the execution of Digestor. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.2

A zipped version of the software site can be downloaded here.

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Developers

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