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  AlignMe-a membrane protein sequence alignment web server

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.

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 Creators:
Stamm, Marcus1, Author           
Staritzbichler, René1, Author           
Khafizov, Kamil1, Author           
Forrest, Lucy R.1, Author           
Affiliations:
1Max Planck Research Group of Computational Structural Biology, Max Planck Institute of Biophysics, Max Planck Society, ou_2068293              

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 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.

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Language(s): eng - English
 Dates: 20142014-03-302014-04-21
 Publication Status: Published online
 Pages: 6
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1093/nar/gku291
 Degree: -

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Title: Nucleic Acids Research
  Other : Nucleic Acids Res.
Source Genre: Journal
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Pages: 6 Volume / Issue: 42 (W1) Sequence Number: - Start / End Page: W246 - W251 Identifier: ISSN: 0301-5610
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000262810