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Schrödinger extension for KNIME Workbench version by Schrödinger

Search a protein sequence database using BLAST
Note: To enable web-based searching, please ensure the option "Allow use of web server for BLAST searches" found in the Jobs panel of Maestro preferences, has been checked.

Backend implementation

scripts/blastCLI.py run by cmdRunner.py
The script blastCLI.py is passed to cmdRunner.py to implement this node.


Include Log in output
Include the BLAST log file in the output
The database that will be searched (PDB or NR from NCBI)
Filter query sequence
Filter query sequence to remove low-complexity regions
Expand non-redundant hits
Expand non-redundant BLAST hits by showing additional PDB sequences that are identical to the original hit

Input Ports

Sequences in Maestro format

Output Ports

BLAST alignments in Maestro format

Best Friends (Incoming)

Best Friends (Outgoing)



To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:


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