

SnS-Align Version 1.0

SnS-Align (Structure and Sequence Alignment) is a tool developed 
in perl, used to align the protein sequences by combining sequence
and structure information at an instance. Given a protein sequence
of an organism, the tool is used to identify its homologue(s) in 
the evolutionarily distant organisms, which might not be found from
either sequence alone or structure alone comparisons. 

1.Installation Instructions

	a) Install perl with Tk and EMBOSS package.

	b) unzip the archive and copy into a directory.

	c) Set the path to the installation directory.

You should be able to run SnS-Align
	a) by double clicking on the file SnS-Align.pl in
	   the installation directory.
			(or)
	b) from the command-line, by typing "SnS-Align.pl".

3.Input

	Query is a FASTA formatted protein sequence. If they are 
	multiple protein sequences, only the first sequence is 
	considered for SnS-Alignment.

	DB is set of FASTA formatted protein sequences, with all of
	which the Query is aligned.

	Choose the Scoring Matrix and Gap penallty as per your 
	requirement. If you are not aware of these, use the default values.

4.Output

	You can see the SnS-algnment in a Graphical User interface. 
	"*" indicates the conservation of secondary structure and 
	"+" indicates the conservation of sequence. You can save the
	alignment in Text format or Post script format by selecting
	the save alignment option.

	If the Database is large, saving in Text format would be a better 
	option. In the text version,
		# - implies alpha-Helix 
		$ - implies beta-Sheet

	You can go for another alignment, by choosing the New Alignment option.