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


BACKGROUND
Executables, source code, and sample data are available at http://socs.biology.gatech.edu/
Ondov
Brian D
BD
School of Biology, Georgia Institute of Technology, 310 Ferst Dr., Atlanta, GA 30332-0230, USA.
Varadarajan
Anjana
A
Passalacqua
Karla D
KD
Bergman
Nicholas H
NH
D030541:Databases, Genetic; D016678:Genome; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA