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Multiple Sequence Viewer

Schrödinger extension for KNIME Workbench version by Schrödinger

Visualize, manipulate, and align multiple sequences and their properties, and perform homology modeling with the aligned sequences. Opens the Multiple Sequence Viewer panel. To send the selected (all if none selected) sequences back to KNIME, click on File->"Send Back to KNIME".

Backend implementation

$SCHRODINGER/run multiseqviewer


Column containing input
Column in the input data table in Maestro, Sequence, PDB, String or Text format
Output Column Structure
Choose the output columns: Output only - Only Output structures
Run command for each input row
If this is checked, MultiSeq Viewer is started for each input row
Command line(s)
MultiSequence Viewer command(s) to be executed
Flow variables can be specified in the command lines.
Ex: If "Command line(s)" has "%myvar1%" and if there exists a flow variable "myvar1" or "MultiSeq|myvar1", then its value will get substituted. All flow variables starting with 'MultiSeq|' will be reset after the node gets executed, so that they wont be passed to the subsequent nodes.

Global commands:
set_font_size <font size in points, 8 to 24>, set_display_boundaries <true> or <false>, set_display_identity <true> or <false>, set_display_similarity <true> or <false>, set_display_homology <true> or <false> , set_display_score <true> or <false>, set_wrapped <true> or <false> , set_ruler <true> or <false>

Note: 'send_to_knime' command writes the output without manual intervention. Specifying 'send_to_knime' followed by 'quit', will write the output and returns to KNIME by exiting 'Multiple Sequence Viewer' panel. This is equivalent to "Send Back to KNIME" menu item.

Sequence commands:
deselect_all_sequences, select_all_sequences, invert_sequence_selection
fetch <pdb_id>

Alignment commands:
delete_all, delete_selected_residues
deselect_all, select_all, invert_selection, expand_selection
find <pattern>
multiple_sequence_alignment, pairwise_alignment
remove_empty_columns, remove_gaps
select_aligned_blocks, select_identities, select_structure_blocks

Color commands:
set_color <color_mode>
where color_mode is one of the following:
residue_type, secondary_structure, similarity, kyte_doolittle, hopp_woods, taylor, maestro

Annotation commands:
add_color_blocks, add_consensus, add_symbols, add_global, add_mean_hydrophobicity
delete_annotations, delete_predictions

Maestro commands:
run_blast, run_pfam, run_ssp

Input Ports

Input in Maestro, Alignment, Sequence, Pdb, String or Text format

Output Ports

Output Data in Alignment, Sequences or Text format


Std output/error
Std output/error

Best Friends (Incoming)

Best Friends (Outgoing)



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