RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix

Background The functions of RNA molecules are mainly determined by their secondary structures. These functions can also be predicted using bioinformatic tools that enable the alignment of multiple RNAs to determine functional domains and/or classify RNA molecules into RNA families. However, the existing multiple RNA alignment tools, which use structural information, are slow in aligning long molecules and/or a large number of molecules. Therefore, a more rapid tool for multiple RNA alignment may improve the classification of known RNAs and help to reveal the functions of newly discovered RNAs. Results Here, we introduce an extremely fast Python-based tool called RNAlign2D. It converts RNA sequences to pseudo-amino acid sequences, which incorporate structural information, and uses a customizable scoring matrix to align these RNA molecules via the multiple protein sequence alignment tool MUSCLE. Conclusions RNAlign2D produces accurate RNA alignments in a very short time. The pseudo-amino acid substitution matrix approach utilized in RNAlign2D is applicable for virtually all protein aligners.

RNAlign2D – a novel RNA structural alignment tool based on pseudo-amino acid substitution matrix

MotivationThe function of RNA molecules is mainly determined by their secondary structure. Addressing that issue requires creation of appropriate bioinformatic tools that enable alignment of multiple RNA molecules to determine functional domains and/or classify RNA families. The existing tools for RNA multiple alignment that use structural information are relatively slow. Therefore, providing a rapid tool for multiple structural alignment may improve classification of the known RNAs and reveal the function of the newly discovered ones.ResultsHere, we developed an extremely fast Python based RNAlign2D tool. It converts RNA sequence and structure to pseudo-amino acid sequence and uses customizable pseudo-amino acid substitution matrix to align RNA secondary structures and sequences using MUSCLE. It is suitable for RNAs containing modified nucleosides and/or pseudoknots. Our approach is compatible with virtually all protein aligners.Availability and implementationRNAlign2D is available from https://github.com/tomaszwozniakihg/rnalign2d. It has been tested on Linux and MacOSX.Supplementary informationSupplementary data are available at Bioinformatics online.

Hubsm: A Novel Amino Acid Substitution Matrix for Comparing Hub Proteins

Sequence alignment algorithms and database search methods use BLOSUM and PAM substitution matrices constructed from general proteins. These de facto matrices are not optimal to align sequences accurately, for the proteins with markedly different compositional bias in the amino acid. In this work, a new amino acid substitution matrix is calculated for the disorder and low complexity rich region of Hub proteins, based on residue characteristics. Insights into the amino acid background frequencies and the substitution scores obtained from the Hubsm unveils the residue substitution patterns which differs from commonly used scoring matrices .When comparing the Hub protein sequences for detecting homologs, the use of this Hubsm matrix yields better results than PAM and BLOSUM matrices. Usage of Hubsm matrix can be optimal in database search and for the construction of more accurate sequence alignments of Hub proteins.