Multiple Sequence Viewer

SchrodingerFreeNodes version 4.1.11.201802140058 by Schrodinger

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

Options

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:
send_to_knime
quit
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:
delete_selected_sequences
deselect_all_sequences, select_all_sequences, invert_sequence_selection
fetch <pdb_id>
hide_selected_sequences
remove_redundant_sequences

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
show_all_sequences
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:
align_structures
propagate_colors
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

Views

Std output/error

Std output/error

Best Friends (Incoming)

• Rule Engine (100 %) PredictorStreamable

Workflows

• Prot build 1-3
• RW protein model building
• 05_Multiple Sequence Viewer
• Node MSV

Installation

To use this node in KNIME, install SchrodingerFreeNodes from the following update site: