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Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications.

ABSTRACT: Here, we report the development of SOCS (short oligonucleotide color space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference genome. SOCS performs its mapping within the context of 'color space', and it maximizes usable data by allowing a user-specified number of mismatches. Sequence census functions facilitate a variety of functional genomics applications, including transcriptome mapping and profiling, as well as ChIP-Seq.Executables, source code, and sample data are available at http://socs.biology.gatech.edu/

SUBMITTER: Ondov BD 

PROVIDER: S-EPMC2639273 | biostudies-other | 2008 Dec

REPOSITORIES: biostudies-other

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Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications.

Ondov Brian D BD   Varadarajan Anjana A   Passalacqua Karla D KD   Bergman Nicholas H NH  

Bioinformatics (Oxford, England) 20081007 23

<h4>Unlabelled</h4>Here, we report the development of SOCS (short oligonucleotide color space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference genome. SOCS performs its mapping within the context of 'color space', and it maximizes usable data by allowing a user-specified number of mismatches. Sequence census functions facilitate a variety of functional genomics applications, including transcriptome mapping and profiling, as well a  ...[more]