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[ Default Alignment | Align Two Sequence | Sequence to Structure Alignment | Align DNA vs Protein | Multiple Sequence Alignment | Drag & Drop ]
To make an alignment using the default parameters:
Alignment parameters (such as alignment method) can be changed using the options in the Bioinfo menu (e.g. Align Two Sequences and Multiple Sequences).
To align two sequences:
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
This option allows you to align a sequence to a template structure sequence using secondary structure weighting.
To align DNA to protein:
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.
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.
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