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Dfi

Generic Workflow Nodes for KNIME: SeqAn version 2.4.1.202004061533 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

The Deferred Frequency Index (DFI) is a tool for string mining under frequency constraints, i.e., predicates that evaluate solely the frequency of a pattern occurrence in the data. The frequency of a pattern is defined as the number of distinct sequences in a database that contain the pattern at least once. Currently the implementation contains 3 different predicates and can easily be extended by user-defined frequency predicates. The frequencies are calculated during the construction of a suffix tree over all databases, which enables to limit the index construction to a problem-specific minimum referred to as the optimal monotonic hull.

Web Documentation for Dfi

Options

version-check: Turn this option off to disable version update notifications of the application.
minmax: Set minimal and maximal frequency per database.
support: Minimal support in the first (with --growth) or all (with --entropy) databases.
growth: Minimal support ratio between the first and second databases.
entropy: Maximal entropy of support values of all databases.
alphabet: Specify database alphabet.
maximal: Output only left and right maximal substrings.

Input Ports

: Database files in Fasta/Fastq or text format (lines are strings). [fq,fastq,fa,fasta,faa,ffn,fna,frn,embl,gbk,raw,sam]

Output Ports

: Change output filename. Default: <stdout>. [txt]

Views

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

Best Friends (Incoming)

Input File (25 %)
Input Files (25 %)
Bisar (25 %)
Double Widget (25 %)

Best Friends (Outgoing)

ComputeGain (50 %)
Stellar (50 %)

Installation

To use this node in KNIME, install SeqAn 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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