Bhat, B., Ganai, N.A., Andrabi, S.M., Shah, R.A. and Singh, A., 2017. TM-Aligner: Multiple sequence alignment tool for transmembrane proteins with reduced time and improved accuracy. Scientific reports, 7(1), p.12543.

Research
03 Apr 2018

TM-Aligner: Multiple sequence alignment tool for transmembrane proteins with reduced time and improved accuracy

 

TM-Aligner (Transmembrane Membrane proteins - Aligner) is a protein sequence alignment tool developed in C, Perl (version 5.20) and PHP (version 5.6). The web interface of TM-Aligner is written in PHP and JavaScript under XAMPP web server running on a Linux system. TM-Aligner uses the progressive alignment strategy for aligning protein sequences. The UPGMA method is used to find similar sequences which guide the alignment process. Time complexity of UPGMA is O(N3), however, time complexity has been reduced to O(N2) by maintaining an array of references to the minimum value in each row of the distance matrix10. TMHMM is used to predict transmembrane regions within the protein sequence. The input protein sequences are divided into cytoplasmic, non-cytoplasmic and transmembrane regions. For aligning divergent sequences, dynamic programming has been found exceptionally superior over K-tuple method therefore, all regions are aligned independently using dynamic programming. The Wu-Manber string matching algorithm is used in stitching transmembrane regions with cytoplasmic and non-cytoplasmic regions. Wu-Manber string matching algorithm sieve through thousands of matches that are found in sequences (or profiles) and determine the largest set of consistent matches that can be included in final alignment

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