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

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 multip...

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Bibliographic Details
Published in:BMC bioinformatics 2021-10, Vol.22 (1), p.1-504, Article 504
Main Authors: Wozniak, Tomasz, Sajek, Malgorzata, Jaruzelska, Jadwiga, Sajek, Marcin Piotr
Format: Article
Language:English
Subjects:
Alignment
Amino acid sequence
Amino acid substitution
Amino acids
Computational biology
Gene expression
Gene sequencing
Matrices
Methods
Nucleotide sequence
Optimization
Proteins
Python (Programming language)
Ribonucleic acid
RNA
RNA 2D structure
RNA alignment
RNA secondary structure alignment
RNA sequencing
Software
Structure
Structure alignment
Substitutes
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Description
Summary: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. 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. 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.
ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-021-04426-8