title: AlignMe--a membrane protein sequence alignment web server.
abstract: 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. Access is available at http://www.bioinfo.mpg.de/AlignMe.
authors.affiliation: Computational Structural Biology Group, Max Planck Institute of Biophysics, Frankfurt am Main 60438, Germany.
authors.forename: Marcus
authors.initials: M
authors.lastname: Stamm
authors.affiliation: Computational Structural Biology Group, Max Planck Institute of Biophysics, Frankfurt am Main 60438, Germany.
authors.forename: René
authors.initials: R
authors.lastname: Staritzbichler
authors.affiliation: Computational Structural Biology Group, Max Planck Institute of Biophysics, Frankfurt am Main 60438, Germany.
authors.forename: Kamil
authors.initials: K
authors.lastname: Khafizov
authors.affiliation: Computational Structural Biology Group, Max Planck Institute of Biophysics, Frankfurt am Main 60438, Germany lucy.forrest@nih.gov.
authors.forename: Lucy R
authors.initials: LR
authors.lastname: Forrest
mesh_terms: D057927:Hydrophobic and Hydrophilic Interactions; D020407:Internet; D008565:Membrane Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D008565:Membrane Proteins
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