Need help with secondary structure mask in Clustal

Mike Noren michael.noren at
Thu Jul 6 16:18:34 EST 2000

I want to use secondary structure information for aligning a set of
18S sequences with ClustalW or ClustalX, but can't get Clustal to
accept the data.

My DNA data is originally in PIR/PEARSON FASTA format, but I've used
Clustal to translate it into GDE and Clustal.

I've then tried to insert my penalty mask into first the GDE file like

GM_sequence1 1232131232312312321111...

... but no go. The clustal help-file says the mask must be specified
as text, but using the full GDE fields to do so just renders the file
unreadable for Clustal.

I then tried translating the sequences to clustal format, and
painstakingly cut&pasted the 6000 digits long penalty mask into the
interleaved alignment

!GM_sequence1     1232131232312312321111...
sequence1               ACGATGATATTAAAGG...

...but still no luck. And yet, as far as I can see, I've completely
duplicated the example in the clustal help.

So, the help file isn't much help, really, and clustal doesn't come
with an example file for this, so...PLEASE could someone send me a
functioning data matrix which incorporates secondary structure

You can delete nearly all the data if you wish, but I really need to
see how the file is supposed to be constructed.

Michael Norén, Doctoral student,
Stockholm University and                      Tel: Int +46 (0)8 5195 4236
Swedish Museum of Natural History,     Fax: Int +46 (0)8 5195 4125
                        "Nihil umquam facile" 

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