Geoseq

Geoseq maps reference sequences against short-read deep-sequencing datasets from public repositories such as the Gene Expression Omnibus (GEO), the Sequence Read Archive (SRA) hosted by NCBI, and the DNA Data Bank of Japan (ddbj) to quantify target sequence abundance and support analyses of mRNA-seq and microRNA datasets.

Key Features:

• Reference Sequence Mapping: Maps reference sequences against sequencing libraries rather than mapping reads to a reference, enabling targeted interrogation of datasets.
• Tiled Query and Coverage Measurement: Reduces input sequences into tiles and measures the coverage of each tile within a sequence library using suffix arrays.
• Controlled Vocabulary Organization: Organizes sequencing libraries using a controlled vocabulary of organism, tissue type, and experimental conditions to facilitate selection of relevant datasets.

Scientific Applications:

• Differential Isoform Expression Analysis: Applied to mRNA-seq datasets to identify differential expression patterns among isoforms.
• MicroRNA Identification: Identifies microRNAs within sequencing libraries, including distinction between mature and star sequences.
• Annotation Verification: Detects potentially mis-annotated miRNAs to support refinement of genomic annotations.

Methodology:

Geoseq maps reference sequences against sequencing data by reducing reference sequences into tiles and measuring tile coverage within sequence libraries using suffix arrays.