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NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes

Stefanie Geisen, Guillermo Barturen, Ángel M. Alganza, Michael Hackenberg, José L. Oliver
2013 Nucleic Acids Research  
The updated release of 'NGSmethDB' (http:// bioinfo2.ugr.es/NGSmethDB) is a repository for single-base whole-genome methylome maps for the best-assembled eukaryotic genomes.  ...  We implemented stringent quality controls to minimize important error sources, such as sequencing errors, bisulfite failures, clonal reads or single nucleotide variants (SNVs).  ...  CONCLUSIONS NGSmethDB provides high-resolution epigenome-wide methylome maps for a collection of the best-assembled eukaryotic genomes.  ... 
doi:10.1093/nar/gkt1202 pmid:24271385 pmcid:PMC3964946 fatcat:6amwg23cfvechfgkjumjx4wujy

HPVbase – a knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas

Amit Kumar Gupta, Manoj Kumar
2015 Scientific Reports  
NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes. Nucleic Acids Res42, D53-59; DOI:10.1093/nar/gkt1202 (2014). 8 microRNAs targets on viruses.  ...  D. et al. miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res42, D78-85; DOI:10.1093/nar/gkt1266 (2014). 26 Szczesniak, M.  ... 
doi:10.1038/srep12522 pmid:26205472 pmcid:PMC4513345 fatcat:7nitzq6ryvgwhjrcutyhknvg3y

Bioinformatics Tools and Genomic Resources Available in Understanding the Structure and Function of Gossypium [chapter]

Venkateswara R. Sripathi, Ramesh Buyyarapu, Siva P. Kumpatla, Abreeotta J. Williams, Seloame T. Nyaku, Yonathan Tilahun, Venu Kalavacharla, Govind C. Sharma
2016 Bioinformatics - Updated Features and Applications  
This discourse begins with a description of concurrent advances in high-throughput genome sequencing and bioinformatics analyses and focuses on four major sections covering bioinformatics tools and resources  ...  The primary goal of this chapter is to provide a review of such tools and resources for analyzing the structure and function of the cotton genome with preferential emphasis on this complex and economically  ...  Ivona Lovric for their valuable suggestions and comments in improving this book chapter.  ... 
doi:10.5772/64325 fatcat:y4svepemajghfddagn535mvpqy

Next-Generation Sequencing: From Understanding Biology to Personalized Medicine

Karen Frese, Hugo Katus, Benjamin Meder
2013 Biology  
Within just a few years, the new methods for high-throughput next-generation sequencing have generated completely novel insights into the heritability and pathophysiology of human disease.  ...  In this review, we wish to highlight the benefits of the current state-of-the-art sequencing technologies for genetic and epigenetic research.  ...  Acknowledgements Our research is supported by grants from the German Ministry of Education and Research (BMBF): NGFN-plus 01GS0836, NGFN-Herz-Kreislauf-German Centre for Cardiovascular Research); the University  ... 
doi:10.3390/biology2010378 pmid:24832667 pmcid:PMC4009863 fatcat:zkakkzgc25benbu2zzenhvbjvm

Sequencing technologies and genome sequencing

Chandra Shekhar Pareek, Rafal Smoczynski, Andrzej Tretyn
2011 Journal of Applied Genetics  
The high-throughput -next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared  ...  With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism  ...  Bhaijee et al. 2011 Database for whole genome methylation maps at single-cytosine resolution: NGS methylation database (NGSmethDB: http://bioinfo2.ugr.es/ NGSmethDB/gbrowse/) for human, mouse and Arabidopsis  ... 
doi:10.1007/s13353-011-0057-x pmid:21698376 pmcid:PMC3189340 fatcat:ocf66v7fv5gdtmir5h35gochaq