View Single Post
Old 10-20-2008, 08:53 PM   #1
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,358
Default SOCS: Efficient mapping of Applied Biosystems SOLiD sequence data to a ref genome...

Bioinformatics. 2008 Oct 7. [Epub ahead of print]

Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications.
Ondov B, Varadarajan A, Passalacqua KD, Bergman NH.

School of Biology, Georgia Institute of Technology, 310 Ferst Dr., Atlanta, GA 30332-0230.

SUMMARY: 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. AVAILABILITY: Executables, source code, and sample data are available at http://socs.biology.gatech.edu/ CONTACT: nickbergman(<AT>)gatech.edu SUPPLEMENTARY INFORMATION: Available at Bioinformatics online.
ECO is offline   Reply With Quote