24. Pash 3.0 Algorythm
Multi-positional hash tables. A. Reads are indexed in a multi-positional hash table.
B. A sliding fixed size genomic window is used
Coarfa et al. BMC Bioinformatics 2010 11:572 doi:10.1186/1471-2105-11-572
25. BSMAP algorithm
Xi and Li BMC Bioinformatics
A) Bisulfite seed table, using the original seed and bisulfite variants as keys and
corresponding coordinates in the reference genome as values. Each read was looked up in
the seed table for potential mapping positions. B) A positional specific mask of the
corresponding reference sequence was generated by setting 01 to C(light blue) and 11 to A,
G, T(black). The original read was masked by a bitwise AND operation with the positional
specific mask. C) The reference sequence and the masked read were compared with a
bitwise XOR operation. Non-zero XOR results were counted as mismatches (red). Bisulfite
alignment is marked in green.
26. BiQ Analyzer - a software tool for DNA
Example of Graphical Tool
Series GSE49149 Query DataSets for GSE49149
Status Public on Jul 08, 2014
Title Genome-wide DNA methylation patterns in
pancreatic ductal adenocarcinoma (PDAC)
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling
Summary Determine methylation pattern in PDAC a
genome-wide analysis was performed in a cohort of 167
PDAC and 29 adjacent pancreatic tissues samples using the
Infinium 450k methylation arrays (Illumina).
Int J Cancer. 2014 Sep 1;135(5):1110-8. doi:
10.1002/ijc.28765. Epub 2014 May 9.
Status Public on Oct 16, 2012
Title Methylation data from glioblastoma tumor samples
Organism Homo sapiens Experiment type Methylation
profiling by genome tiling array
Summary Glioblastoma (GBM) is an incurable brain tumor
carrying a dismal prognosis, which displays considerable
Sturm D, Witt H, Hovestadt V, Khuong-Quang DA et al.
Hotspot mutations in H3F3A and IDH1 define distinct
epigenetic and biological subgroups of glioblastoma. Cancer
Cell 2012 Oct 16;22(4):425-37. PMID: 23079654
64. Hotspot Mutations in H3F3A and IDH1 Define Distinct
Epigenetic and Biological Subgroups of Glioblastoma