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ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
- Source :
- BMC Genomics
- Publication Year :
- 2014
-
Abstract
- Background Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to manifest diverse phenotypes, is key to advancing our understanding of the mammalian genome. Next-generation sequencing technology is now used widely to probe these protein-DNA interactions and to profile gene expression at a genome-wide scale. As the cost of DNA sequencing continues to fall, the interpretation of the ever increasing amount of data generated represents a considerable challenge. Results We have developed ngs.plot – a standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on next-generation sequencing data. We demonstrate that ngs.plot is not only efficient but also scalable. We use a few examples to demonstrate that ngs.plot is easy to use and yet very powerful to generate figures that are publication ready. Conclusions We conclude that ngs.plot is a useful tool to help fill the gap between massive datasets and genomic information in this era of big sequencing data.
- Subjects :
- Epigenomics
Genomics
Computational biology
Biology
Web Browser
DNA sequencing
Plot (graphics)
Workflow
03 medical and health sciences
0302 clinical medicine
Databases, Genetic
Genetics
Animals
Data Mining
Humans
Promoter Regions, Genetic
Embryonic Stem Cells
030304 developmental biology
Visualization
0303 health sciences
Sequence Analysis, RNA
Computational Biology
High-Throughput Nucleotide Sequencing
Reproducibility of Results
Sequence Analysis, DNA
Standalone program
Next-generation sequencing
DNA microarray
030217 neurology & neurosurgery
Algorithms
Software
Genomic databases
Biotechnology
Subjects
Details
- ISSN :
- 14712164
- Volume :
- 15
- Database :
- OpenAIRE
- Journal :
- BMC genomics
- Accession number :
- edsair.doi.dedup.....f1cc1d5bb567bb14a20f7fcfd9043428