Software

Cosearge

Cosearge detects spatial gene co-localization in 3D genome structure data measured by HiC-seq. Cosearge takes as input a HiC contact matrix and gene annotations, and outputs a list of co-localized genes and their statistical significance. [Best poster presentation in IIBMP 2017; manuscript in preparation]

Bisulfighter, ComMet

Bisulfighter is a analysis pipeline for DNA methylation data measured by bisulfite-seq. Bisulfighter uses a probability-based aligner called LAST for read mapping, and detects differentially methylated region (DMR) using ComMet based on hidden Markov model (HMM). [Saito et al. Nucleic Acids Res. 2014; Saito et al. BMC Genomics. 2015]

BPLA Kernel

BPLA Kernel calculates a similarity between RNA sequences. It is a kernel function, and thus can be combined with various kernel-based machine learning methods such as support vector machine (SVM). BPLA Kernel has many applications in noncoding RNA analyses including search from genomic sequences, clustering for finding novel families, and profile-profile comparison. [Morita and Saito et al. Nucleic Acids Res. 2009; Saito et al. BMC Bioinformatics. 2010; etc]