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Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
 Read and Save
 Secondary Structure
 Bioinfo Menu
  Content
  Secondary Structure
  Six Frame Translation
  Set Sequence Type
  Align Two Sequence
  Sequence to Structure Alignment
  Multiple Sequence Alignment
  Profile
  Link to Structure
  Extract Sub-Alignment As Is
  Cut Vertical Alignment Block
  Reorder Sequences
  Extract Unique Sequences
  Load Example Alignment
 BLAST Search
 Sequence Editor
 Alignments
 Editor
 Color Structure by Alignment
Protein Modeling
Cheminformatics
Learn and Predict
Docking
Virtual Screening
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
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Index
PrevICM User's Guide
8.3 Bioinfo Menu
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[ Content | Secondary Structure | Six Frame Translation | Set Sequence Type | Align Two Sequence | Sequence to Structure Alignment | Multiple Sequence Alignment | Profile | Link to Structure | Extract Sub-Alignment As Is | Cut Vertical Alignment Block | Reorder Sequences | Extract Unique Sequences | Load Example Alignment ]

Available in the following product(s): ICM-Pro

Note: Click Next (top right hand corner) to navigate through this chapter. Headings are listed on the left hand side (web version) or by clicking the Contents button on the left-hand-side of the help window in the graphical user interface.

8.3.1 Residue Content


To determine the residue content of a sequence.

  • Bioinfo/Residue Content and a data entry box as shown below will be displayed.
  • Enter the sequence name. See the Load Sequence section for more information on how to load a sequence into ICM using the Graphical User Interface.
  • A table and graph of residue frequencies will be displayed.

8.3.2 Predict Secondary Structure


To predict the secondary structure of a sequence:

  • Bioinfo/Predict Secondary Structure
  • Enter the sequence name. See the Load Sequence section for more information on how to load a sequence into ICM using the Graphical User Interface.
  • An option is provided to ignore currently assigned secondary structure.

To view the secondary structure prediction click on and expand the sequence in the ICM workspace. Regions underlined in red = alpha helix, green = beta sheet, blue = pi helix, magenta = 3/10 helix.

8.3.3 Six Frame Translation


This options returns the translated DNA or RNA sequence ('-' for a Stop codon, 'X' for an ambiguous codon) using the standard genetic code.

  • Read into ICM a DNA sequence from a file (eg File/Open FASTA) or use the File/New option and cut and paste a DNA sequence.
  • Bioinfo/Six Frame Translation
  • Translate all frames or use start codon.

8.3.4 Set Sequence Type


This option allows you to define whether a sequence that is read into ICM is a protein or nucleotide sequence.

  • Read into ICM a sequence (eg File/New and cut and paste sequence or File/Open FASTA)
  • Bioinfo/Set Sequence Type
  • Select the sequence name using the drop down button
  • Select sequence type protein or DNA.

8.3.5 Align Two Sequences


Please see the Alignment Chapter.

8.3.6 Sequence to Structure alignment


Please see the Alignment Chapter.

8.3.7 Multiple Sequence Alignment


Please see the Alignment Chapter.

8.3.8 Alignment Strength Profile


To view a fully interactive alignment strength profile:

  • Create an alignment.
  • Bioinfo/Alignment Strength Profile
  • A fully interactive table and plot will be displayed.

The profile can be plotted onto the alignment:

  • Open the alignment editor panel.
  • Select the plot checkbox and choose either bars or line plot.

8.3.9 Link to Structure


To link a structure to an alignment:

  • Double click on the structure in the ICM workspace to select it.
  • Bioinfo/Link to Structure

NOTE Links are described in more depth in the Making Links Section of the manual.

8.3.10 Extract Sub-Alignment As Is


On occasion you may want to extract a sub alignment from a bigger alignment. For example you wmay only wanto extract the alignment for the sequences linked to a structure.

To extract a sub-alignment:

  • An initial multiple sequence alignment must first be displayed in the graphical user interface.
  • Bioinfo/Extract Sub-Alignment As Is
  • Enter the name of the algienment from which you wish to extract a sub-alignment from.
  • Specify the sequence order numbers you wish to extract - enter each number separated by a space.You can see the sequence order alignment number by selecting the order option in the alignment view options panel. See image below below.
  • Click OK and the extracted sequence alignment will be displayed in a separate alignment tab.

8.3.11 Cut Vertical Alignment Block


To cut a vertical alignment block:

  • An initial alignment must first be displayed in the graphical user interface.
  • Bioinfo/Cut Vertical Alignment Block
  • Enter the alignment from which you wish to cut from.
  • Enter the region of the alignment you wish to cut (from: to:). The easiest way to determine the region to cut is to display the ruler in the alignment. This is an option in the alignemtn view panel - see image below.
  • Click OK and the cut section will be displayed in a new alignment.

8.3.12 Reorder Sequences


To reorder sequences in an alignement

  • An initial multiple sequence alignment must first be displayed in the graphical user interface.
  • Bioinfo/Reorder Sequences
  • Enter the alignment name
  • Enter the new sequence order.You can see the sequence order alignment number by selecting the order option in the alignment view options panel. See image below below.

8.3.13 Extract Unique Sequences


To extract unique sequences from a group of sequences:

  • Read into ICM the sequences you wish to make unique.
  • Select the sequences. A sequence can be selected by double clicking (highlighted blue in ICM workspace) - a range of sequences in the ICM Worskpace can be selected by holding down the SHIFT button and double clicking. A non-contiguous selection can be made by holding down the CTRL button and double clicking.
  • Right click on the sequence selection in the ICM Workspace and select Group sequences
  • Bioinfo/Extract Unique Sequences
  • Enter the name of the sequence group.
  • Enter the number of residue mismatches necesary to determine that a sequence is unique or not.
  • Select whether you want to keep the redundant sequences or delete them from ICM.

8.3.14 Load Example Alignment


To see an example of an alignment select:

  • Bioinfo/Load Example Alignment


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