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AlignMe

Pairwise alignment of membrane protein sequences

Contributors

René Staritzbichler
Marcus Stamm
Kamil Khafizov
Edoardo Sarti
Lucy R. Forrest
Giacomo Fiorin

Required external libraries

Boost library headers, namely shared_ptr.hpp

Optional external code

BLAST - for generating position specific substitution matrices
PSIPRED - for generating secondary structure predictions
OCTOPUS - for generating transmembrane predictions
For more details, refer to install instructions

How to install

  • change directory to the appropriate folder in your terminal
  • type make
  • the alignme executable is created in this folder and ready to use

How to use

  • have a look at the online manual and try out some examples
  • to run AlignMePST jobs, use scripts/use_best_parameters.pl. This script assumes that PSSM, secondary structure predictions, and transmembrane predictions are available.

Online server

Our online server is available at http://www.bioinfo.mpg.de/AlignMe/

If you have questions about the usage of this program or discovered a bug, then please post a message on github or write to: [email protected]

How can I cite AlignMe?

If you have used AlignMe in your work, please cite:

For pairwise alignments:
Stamm M., Staritzbichler R., Khafizov K. and Forrest L.R. 2013 PLoS One

For anchors:
Staritzbichler R., Sarti E., Yaklich E., Aleksandrova A., Stamm M., Khafizov K. and Forrest L.R. 2021 PLoS One

For the alignment of two MSAs:
Khafizov K., Staritzbichler R., Stamm M. and Forrest L.R. 2010, Biochemistry

Release Notes:

Version 1.2

Inclusion of anchors as constraints

Version 1.1

  • Position Specific Subsititution Matrices (PSSMs) supported as an alignment input
  • ClustalW and Fasta-Format output of the aligned sequences supported
  • extraction of two sequences from the alignment of two averaged MSAs possible
  • gaps are now "?0" in the profiles - no more confusion of gaps with profile values having a 0
  • added a perl script with the best parameters for alpha-helical proteins to the package
  • improved error feedback

Version 1.0

  • initial release