Format

Send to

Choose Destination
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W246-51. doi: 10.1093/nar/gku291. Epub 2014 Apr 21.

AlignMe--a membrane protein sequence alignment web server.

Author information

1
Computational Structural Biology Group, Max Planck Institute of Biophysics, Frankfurt am Main 60438, Germany.
2
Computational Structural Biology Group, Max Planck Institute of Biophysics, Frankfurt am Main 60438, Germany lucy.forrest@nih.gov.

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.

PMID:
24753425
PMCID:
PMC4086118
DOI:
10.1093/nar/gku291
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center