BS Seeker

BS Seeker maps bisulfite-treated sequencing reads to reference genomes to enable genome-wide DNA methylation analysis at single-nucleotide resolution.

Key Features:

• Three-Letter Alphabet Conversion: Converts the reference genome into a three-letter alphabet to account for C-to-T changes introduced by bisulfite treatment and facilitate alignment.
• Use of Bowtie: Aligns bisulfite-converted reads to the transformed reference genome using the Bowtie aligner.
• Sequence Tag Handling: Explicitly considers sequence tags generated during certain library construction protocols to reduce mapping ambiguity.
• Post-Processing Quality Control: Performs post-processing to remove non-unique and low-quality mappings.
• Fast Alignment Performance: Reports significantly faster alignment times on human genome mappings compared with RMAP and BSMAP.

Scientific Applications:

• Genome-wide DNA methylation profiling: Enables single-nucleotide resolution methylation analysis from bisulfite sequencing data.
• Benchmarking on diverse datasets: Tested on synthetic data, a bisulfite-converted Arabidopsis thaliana library, and human libraries from two distinct experimental protocols.
• Protocol-versatile read mapping: Maps reads generated by different library construction protocols by leveraging sequence tag information.
• Large mammalian genome studies: Applicable to high-throughput epigenetic studies involving large mammalian genomes.

Methodology:

Converts the reference genome to a three-letter alphabet, aligns reads using Bowtie with consideration of sequence tags from library protocols, and post-processes alignments to remove non-unique and low-quality mappings.