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.
(c) Copyright 2010 by David Weese and Marcel H. Schulz
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
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.)
Installation
To use this node in KNIME, install SeqAn from the following update site:
Developers
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