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Old 06-07-2012, 11:03 AM   #1
joshuapk
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Location: Pittsburgh

Join Date: Mar 2012
Posts: 9
Default Protein Secondary Structure Guided Alignments

So I need to make an alignment using secondary structure for gap penalties. I have found that Clustal is suppose to be able to do this but I try to follow their instructions (http://www.bugaco.com/bioinf/ClustalW/helpB.html) and it does not even read the secondary structure correctly specifically the "." are completely ignored.
If anyone has gotten this to work for them please let me know what you did.
Josh

P.S. Also open to any other program that has this functionality.
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Old 07-04-2014, 08:35 PM   #2
Thanh Hang
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Location: Viet Nam

Join Date: Jul 2014
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Default

Hello everybody!
I'm performing study on activity improvement of alkaline phytase in digestive tract of mono-gastric animals by site-directed mutagenesis.
I need a software associated protein 3D structure pedict
If anyone has gotten this to work for them please let me know what you did
Thanks!
p/s I known yasara, but i can't download it
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