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UnSplicer: mapping spliced RNA-seq reads in compact genomes and filtering noisy splicing

Paul D. Burns, Yang Li, Jian Ma, Mark Borodovsky
2013 Nucleic Acids Research  
To improve detection of splice junctions, TrueSight uses information on statistical patterns of nucleotide ordering in intronic and exonic DNA.  ...  Accurate mapping of spliced RNA-Seq reads to genomic DNA has been known as a challenging problem.  ...  ACKNOWLEDGEMENTS We are very grateful to Alexandre Lomsadze for valuable technical assistance. We thank Susan M.E. Smith for useful comments.  ... 
doi:10.1093/nar/gkt1141 pmid:24259430 pmcid:PMC3936741 fatcat:cqjcgz342vcofl6txuex4saena

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

Alexandre Lomsadze, Paul D. Burns, Mark Borodovsky
2014 Nucleic Acids Research  
The new algorithm, GeneMark-ET augments GeneMark-ES with a novel method that integrates RNA-Seq read alignments into the self-training procedure.  ...  Use of 'assembled' RNA-Seq transcripts is far from trivial; significant error rate of assembly was revealed in recent assessments.  ...  Smith for valuable comments.  ... 
doi:10.1093/nar/gku557 pmid:24990371 pmcid:PMC4150757 fatcat:hazlx3c63zb7fo3kxz7x7ehkte


2014 Der Pathologe  
Moreover, the usefulness of immunohistochemistry is limited, emphasizing the need for better molecular tools to assist in the diagnosis.  ...  No mutations of PIK3CA or AKT1 were detected in LMS, SS and MFS.  ...  For transcriptome analysis (RNA-Seq) of p38 specific genes isoforms were knocked down with specific siRNAs during Arsenite stress induction.  ... 
doi:10.1007/s00292-014-1944-9 fatcat:jxkoidekjjeh7gq2ivyrysuzwe