Profile and structure alignments

By PROFILE ALIGNMENT, we mean alignment using existing alignments. Profile alignments allow you to store alignments of your favourite sequences and add new sequences to them in small bunches at a time. A profile is simply an alignment of one or more sequences (e.g. an alignment output file from CLUSTAL W). Each input can be a single sequence. One or both sets of input sequences may include secondary structure assignments or gap penalty masks to guide the alignment.

The profiles can be in any of the allowed input formats with "-" characters used to specify gaps (except for MSF/RSF where "." is used).

You have to specify the 2 profiles by choosing menu items 1 and 2 and giving 2 file names. Then Menu item 3 will align the 2 profiles to each other. Secondary structure masks in either profile can be used to guide the alignment.

Menu item 4 will take the sequences in the second profile and align them to the first profile, 1 at a time. This is useful to add some new sequences to an existing alignment, or to align a set of sequences to a known structure. In this case, the second profile need not be pre-aligned.

The alignment parameters can be set using menu items 5, 6 and 7. These are EXACTLY the same parameters as used by the general, automatic multiple alignment procedure. The general multiple alignment procedure is simply a series of profile alignments. Carrying out a series of profile alignments on larger and larger groups of sequences, allows you to manually build up a complete alignment, if necessary editing intermediate alignments.

SECONDARY STRUCTURE OPTIONS . Menu Option 0 allows you to set secondary structure parameters. If a solved structure is available, it can be used to guide the alignment by raising gap penalties within secondary structure elements, so that gaps will preferentially be inserted into unstructured surface loop regions. Alternatively, a user-specified gap penalty mask can be supplied for a similar purpose.

A gap penalty mask is a series of numbers between 1 and 9, one per position in the alignment. Each number specifies how much the gap opening penalty is to be raised at that position (raised by multiplying the basic gap opening penalty by the number) i.e. a mask figure of 1 at a position means no change in gap opening penalty; a figure of 4 means that the gap opening penalty is four times greater at that position, making gaps 4 times harder to open.

The format for gap penalty masks and secondary structure masks is explained here