SOCS

SOCS performs un-gapped, color-space mapping of Applied Biosystems SOLiD reads to a reference genome and supports bisulfite sequencing analysis for sequence census and functional genomics applications.

Key Features:

• Color Space Mapping: Leverages the color-space representation inherent to SOLiD sequencing data for read-to-reference alignment.
• Un-gapped Alignment: Performs reference-based un-gapped alignments of short oligonucleotide reads.
• Bisulfite Capability: Supports analysis of bisulfite-treated SOLiD reads for methylation-related studies.
• Mismatch Tolerance: Allows users to specify the number of mismatches permissible during mapping.
• Sequence Census Functions: Provides sequence census functions for quantitative analyses of mapped reads.
• Functional Genomics Support: Enables applications such as transcriptome mapping and profiling and ChIP-Seq analysis.

Scientific Applications:

• Transcriptome mapping and profiling: Mapping and quantitative profiling of transcriptomes from SOLiD sequencing data.
• ChIP-Seq analysis: Mapping reads for chromatin immunoprecipitation sequencing to study protein–DNA interactions.
• Functional genomics: Accurate mapping of high-throughput SOLiD reads to reference genomes for gene expression and regulatory mechanism studies.

Methodology:

Converts raw SOLiD sequence data into color space and aligns reads to a reference genome using un-gapped alignment while accommodating user-defined mismatch thresholds.