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BLAST

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.

Options

Include Log in output: Include the BLAST log file in the output
Database: The database that will be searched (PDB or NR)
Location: Whether to run Blast local (via downloaded or standard blast databases) or remote ( via web connection to NCBI )
Maximum number of hits for remote search: Maximum number of hits to return from remote search (local search has no such limit). The default is 10,000.
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

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Workflows

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Installation

To use this node in KNIME, install the extension Schrödinger Extensions for KNIME from the below update site following our NodePit Product and Node Installation Guide:

v5.7

A zipped version of the software site can be downloaded here.

Plugin provider: Schrödinger

Plugin version: 25.2.133.v202505021925

On NodePit since: 2025-12-25

Last update: 2026-01-08

KNIME versions: v5.7, v5.6, v5.5, v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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