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[ Content | Secondary Structure | Six Frame Translation | Set Sequence Type | Align Two Sequence | Sequence to Structure Alignment | Align DNA vs Protein | Multiple Sequence Alignment | Link to Structure | Extract Sub-Alignment As Is | Cut Vertical Alignment Block | Reorder Sequences | Extract Unique Sequences | Load Example Alignment ]

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.

9.2.1 Residue Content


To determine the residue content of a sequence.

9.2.2 Predict Secondary Structure


To predict the secondary structure of a sequence:

To view the secondary structure prediction click on and expand the sequence in the ICM workspace. Regions underlined in red are helices and green represents beta sheet.

9.2.3 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.

9.2.4 Set Sequence Type


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

9.2.5 Align Two Sequences


To align two sequences:

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.

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)

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

9.2.6 Sequence to Structure alignment


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

9.2.7 Align DNA vs Protein


To align DNA to protein:

9.2.8 Multiple Sequence Alignment


To align more than 2 sequences:

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.

9.2.9 Link to Structure


To link a structure to an alignment:

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

9.2.10 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:

9.2.11 Cut Vertical Alignment Block


To cut a vertical alignment block:

9.2.12 Reorder Sequences


To reorder sequences in an alignement

9.2.13 Extract Unique Sequences


To extract unique sequences from a group of sequences:

9.2.14 Load Example Alignment


To see an example of an alignment select:


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