sRNAbench

sRNAbench processes and analyzes small RNA sequencing data from next-generation sequencing platforms such as Illumina and SOLiD for microRNA, isomiR, and other small RNA expression profiling.

Key Features:

• Comprehensive Protocol Support: Incorporates major RNA library preparation protocols and addresses adapter ligation bias and PCR amplification artifacts.
• Integration of Internal Controls: Supports spike-in sequences for normalization to improve reliability of expression profiling.
• Enhanced Reference Databases: Leverages updated microRNA reference databases that balance accuracy (minimizing false positives) and completeness (reducing false negatives).
• IsomiR Analysis: Detects and analyzes small RNA sequence and length variants, including isomiRs.
• sRNAde Integration: Summarizes multiple aspects of small RNA sequencing studies and detects consensus differential expression patterns across datasets.

Scientific Applications:

• microRNA expression profiling: Quantification and profiling of microRNA expression from small RNA-seq datasets.
• IsomiR discovery and characterization: Identification and analysis of sequence and length variants of small RNAs.
• Normalization using spike-ins: Use of internal spike-in controls for improved normalization and quantitative comparisons.
• Cross-dataset differential expression analysis: Detection of consensus differential expression patterns across multiple small RNA sequencing datasets via sRNAde.

Methodology:

Processes and analyzes small RNA-seq reads from Illumina and SOLiD; incorporates RNA library preparation protocol handling to address adapter ligation bias and PCR amplification artifacts; supports spike-in normalization; leverages updated microRNA reference databases; detects isomiRs; and summarizes study aspects and consensus differential expression using sRNAde.