DecoyDatabase

Creates combined target+decoy sequence database from forward sequence database.

Web Documentation for DecoyDatabase

Options

version: Version of the tool that generated this parameters file.
decoy_string: String that is combined with the accession of the protein identifier to indicate a decoy protein.
decoy_string_position: Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?
only_decoy: Write only decoy proteins to the output database instead of a combined database.
type: Type of sequence. RNA sequences may contain modification codes, which will be handled correctly if this is set to 'RNA'.
method: Method by which decoy sequences are generated from target sequences. Note that all sequences are shuffled using the same random seed, ensuring that identical sequences produce the same shuffled decoy sequences. Shuffled sequences that produce highly similar output sequences are shuffled again (see shuffle_sequence_identity_threshold).
shuffle_max_attempts: shuffle: maximum attempts to lower the amino acid sequence identity between target and decoy for the shuffle algorithm
shuffle_sequence_identity_threshold: shuffle: target-decoy amino acid sequence identity threshold for the shuffle algorithm. If the sequence identity is above this threshold, shuffling is repeated. In case of repeated failure, individual amino acids are 'mutated' to produce a different amino acid sequence.
seed: Random number seed (use 'time' for system time)
enzyme: Enzyme used for the digestion of the sample. Only applicable if parameter 'type' is 'protein'.
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)
missed_cleavages: Number of missed cleavages for relevant and neighbor peptides.
mz_bin_size: Bin size for spectra m/z comparison (the original study suggests 0.05 Th for high-res and 1.0005079 Th for low-res spectra).
pc_mass_tolerance: Maximal precursor mass difference (in Da or ppm; see 'pc_mass_tolerance_unit') between neighbor and relevant peptide.
pc_mass_tolerance_unit: Is 'pc_mass_tolerance' in Da or ppm?
min_peptide_length: Minimum peptide length (relevant and neighbor peptides)
min_shared_ion_fraction: Minimal required overlap 't_i' of b/y ions shared between neighbor candidate and a relevant peptide (t_i <= 2*B12/(B1+B2)). Higher values result in fewer neighbors.
non_shuffle_pattern: Residues to not shuffle (keep at a constant position when shuffling). Separate by comma, e.g. use 'K,P,R' here.
keepPeptideNTerm: Whether to keep peptide N terminus constant when shuffling / reversing.
keepPeptideCTerm: Whether to keep peptide C terminus constant when shuffling / reversing.

Input Ports

: Input FASTA file(s), each containing a database. It is recommended to include a contaminant database as well. [fasta]
: These are the relevant proteins, for which we seek neighbors [fasta,opt.]

Output Ports

: Output FASTA file where the decoy database (target + decoy or only decoy, see 'only_decoy') will be written to. [fasta]
: Output FASTA file with neighbors of relevant peptides (given in 'in_relevant_proteins'). []
: Output FASTA file with target+decoy of relevant peptides (given in 'in_relevant_proteins'). Required for downstream filtering of search results via IDFilter and subsequent FDR. []

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Views

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

Workflows

Developers

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Installation

To use this node in KNIME, install the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v5.3

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

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, ZIB (GKN-Team) and the OpenMS Team

Plugin version: 3.2.0.202409181756

On NodePit since: 2024-10-17

Last update: 2024-11-15

KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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