miRPursuit

miRPursuit analyzes high-throughput small RNA (sRNA) sequencing data to perform end-to-end processing and to identify and annotate conserved and novel sRNA sequences in model and non-model plants.

Key Features:

• End-to-end processing: Automates the workflow from raw sRNA sequencing input to identification and annotation of sRNA sequences.
• Parallel library processing: Processes multiple sRNA libraries concurrently to support comparative analyses of sRNA read accumulation across libraries.
• UNIX shell script implementation: Implements the core workflow as UNIX shell scripts that integrate open-source sRNA analysis software.
• Database integration: Leverages nucleotide sequence resources such as GenBank for comparative sequence analyses and annotation support.
• Configurable parameters: Supports configurable analysis parameters to adapt processing to specific datasets.
• Validation: Validated on datasets from model and non-model plant species.

Scientific Applications:

• Novel and conserved sRNA discovery: Identification and annotation of conserved and novel small RNAs in plant genomes.
• Comparative sRNA profiling: Comparison of sRNA read accumulation across multiple libraries for differential accumulation analyses.
• Plant genomics across species: Application to both model and non-model plants for broad plant genomics and regulatory RNA studies.
• Reference-based annotation: Use of public nucleotide databases such as GenBank to support sequence comparison and annotation.

Methodology:

Core workflow implemented as UNIX shell scripts that integrate open-source sRNA analysis software, perform automated processing from raw sRNA sequencing input to identification and annotation, execute parallel processing of multiple sRNA libraries, and use GenBank for comparative sequence analyses.