BlastR

BlastR searches non-coding RNAs by recoding RNA into protein-like sequences and using a BlosumR di-nucleotide log-odds substitution matrix with the BlastP algorithm to improve sensitivity and specificity.

Key Features:

• Di-Nucleotide Comparison Using BlosumR: Uses BlosumR, a log-odds substitution matrix tailored for RNA, to recode RNA into protein-like sequences enabling di-nucleotide comparisons.
• Integration with BlastP Algorithm: Applies the BlastP algorithm to the protein-like recoded sequences to perform ncRNA searches.
• Performance Benchmarking: Benchmarked against Rfam, demonstrating superior sensitivity over BlastN and outperforming BlastP paired with a single-nucleotide log-odds substitution matrix in both speed and sensitivity.
• Compatibility and Accuracy: With WU-BlastP achieves approximately 5% greater accuracy than WU-BlastN at about 50 times slower speed, and remains effective when used with the NCBI-Blast package.

Scientific Applications:

• ncRNA identification: Identifying non-coding RNAs within large genomic datasets.
• Novel ncRNA discovery: Supporting discovery of novel ncRNA sequences.
• Gene regulation and expression studies: Aiding investigations into ncRNA roles in gene regulation and expression.

Methodology:

Recodes RNA into protein-like sequences leveraging mutual information in di-nucleotides, applies the BlosumR di-nucleotide log-odds substitution matrix and the BlastP algorithm for searches, and benchmarks performance against Rfam with comparisons to BlastN, BlastP (single-nucleotide matrix), WU-BlastP, WU-BlastN, and the NCBI-Blast package.