Performing Alignments

MultiSeq can do both structural and sequence alignments. These options are available via the Tools menu in MultiSeq.

Structure Alignments

MultiSeq uses the program STAMP to structurally align protein molecules. The STAMP algorithm minimizes the $C_\alpha$ distance between aligned residues of each molecule by applying globally optimal rigid-body rotations and translations. Also, note that you can perform alignments on molecules that are structurally similar. If you try to align proteins that have no common structures, STAMP will have no means to align them. If you would like further information about how the alignment occurs, please refer to the STAMP manual (http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/).

Figure 11: STAMP Structural Alignment Window

Align the following:

Choose which structures you wish to align

Number of passes (npass):

Whether one or two fits are to be performed. The idea is that the initial fit can be used with a conformation biased set of parameters to improve the initial fit prior to fitting using distance and conformation parameters. Default NPASS = 2

Similarity (scanscore):

Specifies how the Sc value (STAMP algorithm) is to be calculated. This depends on the particular application. As a general rule of thumb, use SCANSCORE=6 for large database scans, when you are scanning with a small domain, and wishing to find all examples of this domain - even within large structures. Use SCANSCORE=1 when you wish to obtain a set of transformations for a set of domains which you know are similar (and have defined fairly precisely as domains rather than the larger structure that they may be a part of). Default SCANSCORE = 6

Comparison residues (scanslide):

This is the number of residues that a query sequence is 'slid' along a database sequence to derive each initial superimposition. Initially, the N-terminus of the query is aligned to the 1st residue of the databse, once this fit has been performed and refined, and tested for good structural similarity, the N-terminus is aligned with the 1+th position, and the process repeated until the end of the database sequence has been reached. Default SCANSLIDE = 5

Slow scan:

If this box is checked, then the SLOW method of getting the initial fits for scanning will be used (see the manual for mor information). Default SLOWSCAN = FALSE

Defaults:

resets the STAMP parameters to their original values

Sequence Alignments

Sequence alignment in MultiSeq can be done via ClustalW or MAFFT (if you have MAFFT locally installed[For installation information see 1.2.3]) (See Fig. 12).

Figure 12: Sequence Alignment Menu Window

Once you have decided which program to use, you can choose from Multiple Alignment, Profile/Sequence Alignment, or Profile/Profile Alignment. Once you have chosen the desired type of alignment, you can set the proper option.

Multiple Alignment

Choose which sequences or regions you wish to align.

Profile/Sequence Alignment

This requires certain sequences to be marked, and they will then be aligned relative to the group that you specify.

Profile/Profile Alignment

To align one entire group with another entire group, select this option.