Search Results for "epigenetics"

SUPERmerge is a ChIP-seq read pileup analysis and annotation algorithm for investigating alignment (BAM) files of diffuse histone modification ChIP-seq datasets with broad chromatin domains at a single base pair resolution level. SUPERmerge allows flexible regulation of a variety of read pileup parameters, thereby revealing how read islands aggregate into areas of coverage across the genome and what annotation features they map to within individual biological replicates. SUPERmerge is...

MSRE-HTPrimer is an open-source, portable, web-based and easy-to-use tool, which facilitates the design of primer pairs for epigenetic assay design and and genomic sequencing assay design. It uses a simple input and output model and can design primers for hundreds to thousands of target sequences in a single run. Moreover, it does not have any limitations on the number and size of target sequences. MSRE-HTPrimer provides significant improvements over existing solutions with following unique...

...Most genomic sites are represented by short, degenerated motifs with a scattered distribution and sometimes with biological function (ex: regulation of gene expression, splicing patterns or epigenetics signals). These motifs are associated with a huge amount of noise and thus, the development of a computational platform for accurate detection of genomic sites requires the integration of various large-scale biological data in order to filter out false positives. PARSEC represents an intuitive, modular (easily extensible) and all-in-one solution for the efficient integration of lots of diverse genomic information in order to perform nonlinear localization and characterization of biological sites in a user-friendly environment. ...

PDMGE is a software developed for predicting CpG loci and genomic region methylation status. The software is based on Weka project,which extends WEKA to promoter the development of epigenetics. Users should prepare genomic and epigenomic features.