rboAnalyzer

rboAnalyzer extends partial BLAST matches to infer full-length subject sequences and to predict non-coding RNA (ncRNA) homology and secondary structure.

Key Features:

• Extension of Partial Matches: Extends partial BLAST hits to plausible full-length subject sequences for downstream analysis.
• Homology Prediction: Predicts homology between query RNAs and the extended full-length subject sequences.
• Secondary Structure Prediction: Predicts RNA secondary structures by pooling information across homologous RNAs found in BLAST outputs and public databases such as Rfam.
• Input Formats and Custom Databases: Operates on BLAST search results in text format and supports use of custom databases and search options.
• Export Formats: Exports results in various sequence and secondary structure formats.

Scientific Applications:

• ncRNA Homology Discovery: Improves identification and characterization of homologous non-coding RNAs from BLAST search results.
• RNA Secondary Structure Analysis: Supports more reliable secondary structure determination for ncRNAs by leveraging homologous sequence information and Rfam annotations.
• Evolutionary and Functional Inference: Enables inference of evolutionary relationships and functional similarities among ncRNAs.
• Sequence Reconstruction and Annotation: Facilitates reconstruction of full-length sequences from partial BLAST matches for downstream curation and annotation.

Methodology:

Extends partial BLAST matches into plausible full-length subject sequences; predicts homology between query RNAs and extended subjects; predicts secondary structures by pooling information across homologous RNAs from BLAST outputs and Rfam; accepts BLAST text-format input and exports sequence and secondary-structure formats.