TM-MSAligner: A Tool for Multiple Sequence Alignment of Transmembrane Proteins

Transmembrane proteins (TMPs) are crucial to cell biology, making up about 30% of all proteins based on genomic data. Despite their importance, most of the available software for aligning protein sequences focuses on soluble proteins, leaving a gap in tools specifically designed for TMPs. Only a few methods target TMP alignment, with just a couple of the available to researchers. Considering that there are a few particular differences that ought to be taken into consideration aligning TMPs sequences, standard MSA methods are ineffective to align TMPs. In this paper, we present TM-MSAligner, a software tool designed to deal with the multiple sequence alignment of TMPs by using a multi-objective evolutionary algorithm. Our software include features such as transmembrane substitution matrix dynamically used according to the topology region, a high penalty to gap opening and extending, and two MSA quality scores, Sum-Of-Pairs with Topology Prediction and Aligned Segments, that can be optimized at the same time. This approach reduce the number of Transmembrane (TM) and non-Transmembrane (non-TM) broken regions and improve the TMP quality score. TM-MSAligner outputs the results in an HTML format, providing an interactive way for users to visualize and analyze the alignment. This feature allows for the easy identification of each topological region within the alignment, facilitating a quicker and more effective analysis process for researchers.