Geoseq: a tool for dissecting deep-sequencing datasets

Background: Datasets generated on deep-sequencing platforms have been deposited in various public repositories such as the Gene Expression Omnibus (GEO), Sequence Read Archive (SRA) hosted by the NCBI, or the DNA Data Bank of Japan (ddbj). Despite being rich data sources, they have not been used much due to the difficulty in locating and analyzing datasets of interest. Results: Geoseq http://geoseq.mssm.edu provides a new method of analyzing short reads from deep sequencing experiments. Instead of mapping the reads to reference genomes or sequences, Geoseq maps a reference sequence against the sequencing data. It is web-based, and holds pre-computed data from public libraries. The analysis reduces the input sequence to tiles and measures the coverage of each tile in a sequence library through the use of suffix arrays. The user can upload custom target sequences or use gene/miRNA names for the search and get back results as plots and spreadsheet files. Geoseq organizes the public seque...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: James Gurtowski, Anthony Cancio, Hardik Shah, Chaya Levovitz, Ajish George, Robert Homann, Ravi Sachidanandam
• Keywords: BMCBI 2010, Public Datasets, Sequences, Sequencing Data