Pairwise alignment of membrane protein sequences
René Staritzbichler
Marcus Stamm
Kamil Khafizov
Edoardo Sarti
Lucy R. Forrest
Giacomo Fiorin
Boost library headers, namely shared_ptr.hpp
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
- change directory to the appropriate folder in your terminal
- type
make - the
alignmeexecutable is created in this folder and ready 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.
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: AlignMe@rzg.mpg.de
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
Inclusion of anchors as constraints
- 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
- initial release