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Alignment Reader

Schrödinger extension for KNIME Workbench version by Schrödinger

Read alignment files in FASTA and Maestro format. The input format is determined by the file extension. Note that alignments are converted to Maestro format by default.

Backend implementation

seqconvert is used to convert FASTA input to Maestro Alignment format (if necessary)


Alignments file
Alignments file to be loaded
File can be an URL like:
knime://LOCAL/path/to/file - knime://LOCAL refers to the current workspace
knime://knime.workflow/path/to/file - knime://knime.workspace refers to the current workflow
Load all Alignments into one cell
Read Alignments into one table row/cell; the default is to store at most one Alignment per row
Import all Alignments
Whether the entire file should be loaded
If not all Alignments are loaded, which number Alignment, should loader start at (disabled if Import all Alignments is set)
Should the file be loaded until to end (disabled if Import all Alignments is set)
If not all Alignments are imported and not loaded until the end, how many total Alignments should be loaded (disabled if Import all Alignments or End is set)

Output Ports

Alignments in Maestro format

Best Friends (Outgoing)



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