Oligomap

Oligomap locates perfect and single-error (mismatch, insertion, or deletion) matches of small RNAs in sequence databases to enable annotation and comparative expression profiling of small RNA libraries.

Key Features:

• Fast identification: Rapidly locates nearly-perfect matches of small RNAs, including perfect and single-error matches.
• Error model: Treats single errors as mismatches, insertions, or deletions when reporting near matches.
• Algorithm: Employs a fast algorithm specifically tailored for finding nearly-perfect small RNA matches in sequence databases.
• Scalability: Optimized for large-scale datasets with optimal performance when processing approximately 500,000 query sequences.
• Annotation and profiling: Supports annotation of small RNA libraries and expression profiling derived from large-scale sequencing.
• Expression comparison: Implements a Bayesian method to compare small RNA expression across different samples.

Scientific Applications:

• Small RNA identification: Identification of microRNAs (miRNAs), RNA interference small interfering RNAs (rasiRNAs), PIWI-interacting RNAs (piRNAs), and 21U RNAs.
• Novel discovery and annotation: Discovery and annotation of novel small RNAs from large-scale sequencing efforts.
• Deep sequencing analysis: Analysis of deep sequencing libraries that can yield up to a billion nucleotides per library.
• mRNA expression profiling alternative: Computational alternative to oligonucleotide microarray technology for mRNA expression profiling using sequencing-derived data.

Methodology:

Uses a fast algorithm tailored to find nearly-perfect matches (perfect and single-error matches where errors are mismatches, insertions, or deletions), supports annotation of small RNA libraries, and applies a Bayesian method to compare small RNA expression across samples, with optimal performance around 500,000 query sequences.