Sequence and Secondary Structure Alignment program

Dr. Shane Sturrock see.signature at bottom.of.message
Thu Oct 9 14:26:42 EST 1997

Announcing sss_align - Sequence and Secondary Structure Alignment.

A program for performing Smith/Waterman based alignment of sequences
with the addition of secondary structure prediction to allow it to
detect significant sequence identities as low as 15% (CASP2
competition), the grey area for normal sequence analysis is around
25-30% identity.

It was not intended to compete with fold threading algorithms instead
allowing the alignment of sequences where no known structure exists but
where both have secondary structure predictions.  It can also search
against a database derived from real structures (sssdb) where its
sensitivity is similar to fold threading algorithms despite being far
less compute intensive (I have run it on my 486 DX 33 Linux box with no

For an example of its use in the published literature see Nucleic Acids
Research, 1997, Vol 25, No. 17, pp 3408-3414: A prediction of the amino
acids and structures involved in DNA recognition by type I DNA
restriction and modification enzymes, Shane S. Sturrock and David T.F.

The program and associated database creation files are available by
anonymous ftp from in /pub/sss_align

Versions for SGI, SPARCSolaris, SPARCLinux and i386Linux are available. 
Sorry, no Windows or Mac version, I doubt users of those machines would
like the command line interface anyway :-)

The program is still in development but its about time it got some beta
testing! I have included an html users guide which provides some useful
pointers and can also be found at

I hope you find it useful.  If you do, or if you have any comments,
please feel free to e-mail me.

Dr. Shane Sturrock - sss at
The eternal question of what OS to use, MacOS or Windows, has finally 
been answered.  I have no desire to use such toy systems and as such 
choose to use neither, Unix is the answer, now what's the question?

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