AlignMe

			
		

		
	

















AlignMe (for Alignment of Membrane Proteins) is a very flexible sequence alignment program that allows the use of various different measures of similarity. These similarity measures include: substitution matrices, hydrophobicity scales and any kind of profiles (i.e. secondary structure predictions or transmembrane predictions).



AlignMe can be used to examine detailed similarity between homologous proteins even if there is no notable sequence similarity. The predefined gap/weight sets have been optimized for membrane proteins, and so should be particularly useful for these difficult cases.



Help can be found in any section of the forms by clicking on the red buttons. Examples can be processed by clicking on the Example-Button on top of each section. Additionally there is a FAQ! 





Modes of usage:





 a)      AlignMe pairwise- pairwise (PW) alignment of two sequences, using any combination of scales and profiles 


 b)  AlignMe profile-profile- profile-profile (PP) alignment of two multiple sequence alignments





Download AlignMe 1.1 



  source code download of AlignMe 1.1 incl. examples 



  manual for the standalone version of AlignMe 1.1 

A changelog and older versions are available on 
www.forrestlab.org/software_databases.html




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Sign up for our newsletter about AlignMe! It's the best way to stay informed about upcoming updates of AlignMe, improvements of the algorithm as well as new applications of AlignMe (i.e. database search). 



  
    
    
    
    
    
    
    
    
    
    
  
	
		

			
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AlignMe was written in C++ in the  Forrest lab by:

Rene Staritzbichler, Marcus Stamm and Kamil Khafizov 





Stamm M, Staritzbichler R, Khafizov K, Forrest LR (2013) PLoS ONE 8(3): e57731. doi:10.1371/journal.pone.0057731  


Khafizov K., Staritzbichler R., Stamm M. and L.R. Forrest; Biochemistry, 2010, 49(50), 10702-10713 




AlignMe@rzg.mpg.de