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BSMAP: whole genome bisulfite sequence MAPping program.

Xi Y, Li W - BMC Bioinformatics (2009)

Bottom Line: However, mapping high-throughput bisulfite reads to the reference genome remains a great challenge due to the increased searching space, reduced complexity of bisulfite sequence, asymmetric cytosine to thymine alignments, and multiple CpG heterogeneous methylation.BSMAP is the first general-purpose bisulfite mapping software.It is able to map high-throughput bisulfite reads at whole genome level with feasible memory and CPU usage.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Biostatistics, Dan L Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. yxi@bcm.edu

ABSTRACT

Background: Bisulfite sequencing is a powerful technique to study DNA cytosine methylation. Bisulfite treatment followed by PCR amplification specifically converts unmethylated cytosines to thymine. Coupled with next generation sequencing technology, it is able to detect the methylation status of every cytosine in the genome. However, mapping high-throughput bisulfite reads to the reference genome remains a great challenge due to the increased searching space, reduced complexity of bisulfite sequence, asymmetric cytosine to thymine alignments, and multiple CpG heterogeneous methylation.

Results: We developed an efficient bisulfite reads mapping algorithm BSMAP to address the above issues. BSMAP combines genome hashing and bitwise masking to achieve fast and accurate bisulfite mapping. Compared with existing bisulfite mapping approaches, BSMAP is faster, more sensitive and more flexible.

Conclusion: BSMAP is the first general-purpose bisulfite mapping software. It is able to map high-throughput bisulfite reads at whole genome level with feasible memory and CPU usage. It is freely available under GPL v3 license at http://code.google.com/p/bsmap/.

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Related in: MedlinePlus

Mapping bisulfite reads to 4 possible bisulfite strands (BSW/BSWR/BSC/BSCR) is equivalent to mapping the bisulfite read and its reverse complementary read to both Watson/Crick strands of the original reference sequence.
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Figure 4: Mapping bisulfite reads to 4 possible bisulfite strands (BSW/BSWR/BSC/BSCR) is equivalent to mapping the bisulfite read and its reverse complementary read to both Watson/Crick strands of the original reference sequence.

Mentions: As discussed earlier, each bisulfite read needs to be aligned to four bisulfite strands (BSW, BSWR, BSC, BSCR) instead of two normal strands (Watson and Crick) as in normal read mapping. In BSMAP, each bisulfite read and its reverse complementary sequence are aligned with both the Watson and the Crick strands of the reference sequence. This procedure is equivalent to mapping BS reads to four bisulfite strands (BSW, BSWR, BSC, and BSCR) (Figure 4).


BSMAP: whole genome bisulfite sequence MAPping program.

Xi Y, Li W - BMC Bioinformatics (2009)

Mapping bisulfite reads to 4 possible bisulfite strands (BSW/BSWR/BSC/BSCR) is equivalent to mapping the bisulfite read and its reverse complementary read to both Watson/Crick strands of the original reference sequence.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2724425&req=5

Figure 4: Mapping bisulfite reads to 4 possible bisulfite strands (BSW/BSWR/BSC/BSCR) is equivalent to mapping the bisulfite read and its reverse complementary read to both Watson/Crick strands of the original reference sequence.
Mentions: As discussed earlier, each bisulfite read needs to be aligned to four bisulfite strands (BSW, BSWR, BSC, BSCR) instead of two normal strands (Watson and Crick) as in normal read mapping. In BSMAP, each bisulfite read and its reverse complementary sequence are aligned with both the Watson and the Crick strands of the reference sequence. This procedure is equivalent to mapping BS reads to four bisulfite strands (BSW, BSWR, BSC, and BSCR) (Figure 4).

Bottom Line: However, mapping high-throughput bisulfite reads to the reference genome remains a great challenge due to the increased searching space, reduced complexity of bisulfite sequence, asymmetric cytosine to thymine alignments, and multiple CpG heterogeneous methylation.BSMAP is the first general-purpose bisulfite mapping software.It is able to map high-throughput bisulfite reads at whole genome level with feasible memory and CPU usage.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Biostatistics, Dan L Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA. yxi@bcm.edu

ABSTRACT

Background: Bisulfite sequencing is a powerful technique to study DNA cytosine methylation. Bisulfite treatment followed by PCR amplification specifically converts unmethylated cytosines to thymine. Coupled with next generation sequencing technology, it is able to detect the methylation status of every cytosine in the genome. However, mapping high-throughput bisulfite reads to the reference genome remains a great challenge due to the increased searching space, reduced complexity of bisulfite sequence, asymmetric cytosine to thymine alignments, and multiple CpG heterogeneous methylation.

Results: We developed an efficient bisulfite reads mapping algorithm BSMAP to address the above issues. BSMAP combines genome hashing and bitwise masking to achieve fast and accurate bisulfite mapping. Compared with existing bisulfite mapping approaches, BSMAP is faster, more sensitive and more flexible.

Conclusion: BSMAP is the first general-purpose bisulfite mapping software. It is able to map high-throughput bisulfite reads at whole genome level with feasible memory and CPU usage. It is freely available under GPL v3 license at http://code.google.com/p/bsmap/.

Show MeSH
Related in: MedlinePlus