Aug 11 2015 Feedback.
Contents
 
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
 Read and Save
 Secondary Structure
 Bioinfo Menu
 BLAST Search
 Alignments
  Default Alignment
  Align Two Sequence
  Sequence to Structure Alignment
  Align DNA vs Protein
  Multiple Sequence Alignment
  Drag & Drop
 Editor
Tutorials
 
Index
PrevICM User's Guide
6.5 Sequence Alignments
Next

[ Default Alignment | Align Two Sequence | Sequence to Structure Alignment | Align DNA vs Protein | Multiple Sequence Alignment | Drag & Drop ]

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

6.5.1 Default Alignment


To make an alignment using the default parameters:

  • Read in the sequences you wish to align.
  • Select the sequences in the ICM workspace.
  • Right click and choose "Align Sequences".
.

Alignment parameters (such as alignment method) can be changed using the options in the Bioinfo menu (e.g. Align Two Sequences and Multiple Sequences).

6.5.2 Align Two Sequences


To align two sequences:

  • Read into ICM two or more sequences.
  • Bioinfo/Align Two Sequences

  • Enter the name of your first sequence in the 'Sequence 1' data entry box.
  • Enter the name of your second sequence in the 'Sequence 2' data entry box.

NOTE: Any sequences already loaded into ICM can be seen by clicking on the down arrow next to the 'Sequence 1 and 2' data entry boxes. This can save typing and trying to remember what you called your sequence.

  • Enter a unique alignment name in the 'alignmentName' data entry box.
  • Select a comparison matrix from the list shown below by clicking on the arrow next to the 'comp matrix' data entry box.

  • Select the alignment algorithm you wish to use from the list shown below by clicking on the arrow next to the 'alignmentAlgorithm' data aentry box.

ZEGA - a Zero End-gap Global Alignment, that is a pairwise alignment method based on the Needleman and Wunsch algorithm modified to use zero gap end penalties. This type of alignment was first described by Michael Waterman, who called it the "fit" alignment. The paper of Abagyan and Batalov, 1997 describes the statistics of the structural significance of the alignment score and optimization of the alignment parameters for the best recognition of structurally related proteins.

H-Align - alignment method used in the Align and Score functions and find database command (as described in Batalov and Abagyan, 1999)

  • Enter the values you wish to use for Gap Open, Gap Extension and the maximum penalized gap penalty.

Gap Open The absolute gap penalty is calculated as a product of gapOpen and the average diagonal element of the residue comparison table You may vary gapOpen between 1.8 and 2.8 to analyze dependence of your alignment on this parameter. Lower pairwise similarity may require somewhat lower gapOpen parameter. A value of 2.4 (gapExtension=0.15) was shown to be optimal for structural similarity recognition with the Gonnet et. al.) matrix, while a value of 2.0 was optimal for the Blosum50) matrix ( Abagyan and Batalov, 1997).

Gap Extension The absolute gap penalty is calculated as a product of gapExtension and the average diagonal element of the residue comparison table.

maxPenalizedGap The maximum penalized gap which is used for Gap Open and Extension

  • Click OK and the alignment will be displayed in the alignment editor window at the bottom of the graphical user interface.
  • Remember to save the project or write the alignment if you wish to keep the alignment for use at another time.

6.5.3 Sequence to Structure alignment


This option allows you to align a sequence to a template structure sequence using secondary structure weighting.

  • Read into ICM the sequence (ModelSeq) you wish to align to the template sequence.
  • Read in the template (TemplateSeq) structure and extract the sequence from this structure
  • Bioinfo/Sequence to Structure Alignment
  • Enter the ModelSeq and the TemplateSeq name
  • Enter the name you wish to call the alignment.
  • Enter the weights you wish to use for apha and beta secondary structure. The default values have been very well tested.
  • This function uses a dynamic algorithm to find the alignment of the locally structurally similar backbone conformations. The RMSD is calculated within a certain residue window. The default is 3.
  • Press OK and the alignement will be displayed in the bottom of the gui interface.

6.5.4 Align DNA vs Protein


To align DNA to protein:

6.5.5 Multiple Sequence Alignment


To align more than 2 sequences:

  • Read into ICM the sequences you wish to align.
  • Select the sequences you wish to align in the ICM workspace. 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.
  • Bioinfo/Multiple Sequence Alignment
  • Enter the name of the sequence group. If you selected the sequences as described above then the name of the group is selection. Other named groups of sequences can be made by right clicking on the sequence selection.
  • Select the comparison matrix you would like to use.
  • Enter Gap open and extension values.

Gap Open The absolute gap penalty is calculated as a product of gapOpen and the average diagonal element of the residue comparison table You may vary gapOpen between 1.8 and 2.8 to analyze dependence of your alignment on this parameter. Lower pairwise similarity may require somewhat lower gapOpen parameter. A value of 2.4 (gapExtension=0.15) was shown to be optimal for structural similarity recognition with the Gonnet et. al.) matrix, while a value of 2.0 was optimal for the Blosum50) matrix ( Abagyan and Batalov, 1997).

Gap Extension The absolute gap penalty is calculated as a product of gapExtension and the average diagonal element of the residue comparison table.

6.5.6 Drag and Drop


An easy way to add another sequence to an alignment is to drag and drop a loaded sequence from the ICM workspace panel to the alignment window. The sequence automatically becomes part of the alignment.


Prev
BLAST Search
Home
Up
Next
Editor

Copyright© 1989-2015, Molsoft,LLC - All Rights Reserved.
This document contains proprietary and confidential information of Molsoft, LLC.
The content of this document may not be disclosed to third parties, copied or duplicated in any form,
in whole or in part, without the prior written permission from Molsoft, LLC.