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PairAlign

Generic Workflow Nodes for KNIME: SeqAn version 2.3.2.201707261654 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

The program allows one to align two sequences using dyamic programming alignment algorithms while tweaking various parameters.

Web Documentation for PairAlign

Options

version-check
Turn this option off to disable version update notifications of the application.
alphabet
Sequence alphabet.
method
DP alignment method: Needleman-Wunsch, Gotoh, Smith-Waterman, Longest Common Subsequence
gop
Gap open penalty.
gex
Gap extension penalty.
matrix
Score matrix.
msc
Match score.
mmsc
Mismatch penalty.
low
Lower diagonal.
high
Upper diagonal.
config
Alignment configuration.

Input Ports

FASTA file with two sequences. [fa,fasta,faa,ffn,fna,frn]

Output Ports

Output filename. [fa,fasta,faa,ffn,fna,frn,msf,Inactive]

Views

PairAlign Std Output
The text sent to standard out during the execution of PairAlign.
PairAlign Error Output
The text sent to standard error during the execution of PairAlign. (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)

Update Site

To use this node in KNIME, install Generic Workflow Nodes for KNIME: SeqAn from the following update site:

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