PMFastR

PMFastR constructs multiple RNA structure alignments by iteratively integrating sequence and secondary-structure information to align a known-structure sequence against a database of related sequences and enforce structural constraints.

Key Features:

• Iterative Sequence-Structure Alignment: Integrates sequence and structure information in an iterative process to build multiple RNA structure alignments and align sequences with known structures against related-family databases while accounting for structural constraints.
• Efficient Memory Usage: Employs low memory consumption to enable alignments of large RNA sequences, including 16S and 23S rRNAs, on modest hardware.
• Multicore Environment Utilization: Designed to take advantage of multicore processing environments to enhance performance and scalability for complex datasets.

Scientific Applications:

• Benchmark evaluation (BRAliBase): Tested using benchmark datasets from BRAliBase to assess alignment performance relative to other RNA alignment methods.
• Rfam seed regeneration: Demonstrated by automated regeneration of 607 Rfam seed alignments with results comparable to manually curated Rfam seeds.

Methodology:

Start from a single sequence with known structure, align it against a family database, and iteratively refine the multiple alignment by integrating sequence and structural data.