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Title

TM-MOTIF: an alignment viewer to annotate predicted transmembrane helices and conserved motifs in aligned set of sequences

 

Authors

Balasubramanian Nagarathnam1, Kannan Sankar2, Varadhan Dharnidharka3, Veluchamy Balakrishnan4, Govindaraju Archunan5 Ramanathan Sowdhamini1*

 

Affiliation

1National Center for Biological Sciences (TIFR), UAS-GKVK Campus, Bellary Road, Bangalore 560 065, India; 2Birla Institute of Technology and Science, Pilani, India; Presently in: Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA; 3R.V. College of Engineering, Mysore Road, Bangalore, India; Presently in: Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, USA; 4Department of Biotechnology, K.S.Rangasamy College of Technology, KSR. Kalvi Nagar, Tiruchengode - 637215, Tamilnadu, India; 5Department of Animal Science, Bharathidasan University,Trichirapalli, Tamil Nadu, 620 024, India

 

Email

mini@ncbs.res.in; *Corresponding author

 

Article Type

Software

 

Date

Received October 12, 2011; Accepted October 21, 2011; Published October 31, 2011

 

Abstract

Multiple sequence alignments become biologically meaningful only if conserved and functionally important residues and secondary structural elements preserved can be identified at equivalent positions. This is particularly important for transmembrane proteins like G-protein coupled receptors (GPCRs) with seven transmembrane helices. TM-MOTIF is a software package and an effective alignment viewer to identify and display conserved motifs and amino acid substitutions (AAS) at each position of the aligned set of homologous sequences of GPCRs. The key feature of the package is to display the predicted membrane topology for seven transmembrane helices in seven colours (VIBGYOR colouring scheme) and to map the identified motifs on its respective helices /loop regions. It is an interactive package which provides options to the user to submit query or pre-aligned set of GPCR sequences to align with the reference sequence, like rhodopsin, whose structure has been solved experimentally. It also provides the possibility to identify the nearest homologue from the available inbuilt GPCR/OR cluster dataset whose association is already known for its receptor type.

 

Availability

Package is available upon request to mini@ncbs.res.in

 

Keywords

Transmembrane helices, Membrane topology, Amino acid conservation and substitutions, GPCR cluster association

 

Citation

Nagarathnam et al. Bioinformation 7(5): 214-221 (2011)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

Copyright

Publisher

 

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

 

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.