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AlignMe-a membrane protein sequence alignment web server

MPG-Autoren
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Stamm,  Marcus
Max Planck Research Group of Computational Structural Biology, Max Planck Institute of Biophysics, Max Planck Society;

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Staritzbichler,  René
Max Planck Research Group of Computational Structural Biology, Max Planck Institute of Biophysics, Max Planck Society;

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Khafizov,  Kamil
Max Planck Research Group of Computational Structural Biology, Max Planck Institute of Biophysics, Max Planck Society;

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Forrest,  Lucy R.
Max Planck Research Group of Computational Structural Biology, Max Planck Institute of Biophysics, Max Planck Society;

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Zitation

Stamm, M., Staritzbichler, R., Khafizov, K., & Forrest, L. R. (2014). AlignMe-a membrane protein sequence alignment web server. Nucleic Acids Research, 42(W1), W246-W251. doi:10.1093/nar/gku291.


Zitierlink: http://hdl.handle.net/11858/00-001M-0000-0026-B1BC-1
Zusammenfassung
We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences.