SHOWALIGNP

Displays a multiple sequence alignment

showalign displays an aligned set of protein or a nucleic acidsequences in a style suitable for publication.

The output is sent to the screen by default for the user to view, but itcan write the results to a file.

The output highlights various differences or similarities between eachof the sequences and a reference sequence by setting selected types ofmatches to a reference sequence to be '.' characters.

The reference sequence can be either the calculated consensus sequence(the default) or it can be one of the set of aligned sequences,specified by either the ordinal number of that sequence in the inputfile, or by its name.

The output sequences can be displayed in either the input order (thedefault) or they can be sorted in order of their similarity to thereference sequence or sorted alphabetically by their names.

By using the '-show' option, the displayed sequences can either be shown as:

• complete (-show=All),
• only identical matches betweenthe sequence and the reference sequence, all other positions beingreplaced by '.' characters (-show=Identities)
• non-identical matches, with identical matches being replaced by '.'characters, similar matches are shown in lower case (-show=Non-identities)
• similar matches, with non-similar matches being replaced by '.' characters, similar matches are shown in lower case (-show=Similarities)
• dissimilar matches, with identical or similar matches being replaced by '.' characters (-show=Dissimilarities)

A small table of the way these alignments are displayed illustrates this.
If we have a reference protein sequence of "III" and a sequence alignedto this of "ILW", then we have an identical matching residue, then asimilar one, then a dissimilar one.
The different methods of display would give the following:

Reference       IIIAll             ILwIdentical       I..Non-id          .lWSimilar         Il.Dissimilar      ..W

Changing the similar matches to lowercase can optionally be disable byusing the option -nosimilarcase.

The displayed sequence can be numbered by placing a ruler with ticksabove the sequence.

The width of a line can be set. The width of a margin to the left ofthe sequences that shows the sequence names can be set.

Specified regions of the sequence can be displayed in uppercase tohighlight them.

The output can be formatted for HTML.

If the output is being formatted for HTML, then specified regions of thesequence can be displayed in any valid HTML colours.

The consensus line

The uppercase consensus symbol is meant to indicate that the consensusis strong and lowercase indicates that it is weak. In practice, I don'treally like this feature and genarally turn it off.

The cutoff for setting the case of the consensus is set by the qualifier'-setcase'. If the score of the matches is above this value, then thesymbol is in uppercase, iot the score is below the -setcase value thenthe symbol is in lowercase.

To put all of the consensus symbols into uppercase or lowercase, make-setcase very low (try -100000 ?) or very large (try 100000 ?).