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10.1093/bioinformatics/btv510 http://scihub22266oqcxt.onion/10.1093/bioinformatics/btv510 C4896364!4896364!26319390     free     free     free Deprecated: Implicit conversion from float 213.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 213.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       Bioinformatics 2016 ; 32 (7): 1001-8 Nephropedia Template TP {{tp|p=26319390|t=2016. Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis |pdf=|usr=}}{{26319390}} gab.com Text Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis JO: Bioinformatics http://www.kidney.de/pget.php?&tw=1&pmid=26319390 #FOAvip Motivation: Metagenomics research has accelerated the studies of microbial organisms, providing insights into the composition and potential functionality of various microbial communities. Metatranscriptomics (studies of the transcripts from a mixture of microbial species) and other meta-omics approaches hold even greater promise for providing additional insights into functional and regulatory characteristics of the microbial communities. Current metatranscriptomics projects are often carried out without matched metagenomic datasets (of the same microbial communities). For the projects that produce both metatranscriptomic and metagenomic datasets, their analyses are often not integrated. Metagenome assemblies are far from perfect, partially explaining why metagenome assemblies are not used for the analysis of metatranscriptomic datasets.Results: Here, we report a reads mapping algorithm for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction k-mers (k-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph. We developed an application of this mapping algorithm: a reference-based approach to metatranscriptome assembly using graphs of metagenome assembly as the reference. Our results show that this new approach (called TAG) helps to assemble substantially more transcripts that otherwise would have been missed or truncated because of the fragmented nature of the reference metagenome.Availability and implementation: TAG was implemented in C++ and has been tested extensively on the Linux platform. It is available for download as open source at http://omics.informatics.indiana.edu/TAG.Contact:yye@indiana.edu Twit Text FOAVip Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis ????Bioinformatics http://www.kidney.de/pget.php?&tw=1&pmid=26319390 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=26319390 #FOAvip English Wikipedia <ref>{{Cite pmid|26319390}}</ref> Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis #MMPMID26319390 Ye Y; Tang H Bioinformatics 2016[Apr]; 32 (7): 1001-8 PMID26319390show ga Motivation: Metagenomics research has accelerated the studies of microbial organisms, providing insights into the composition and potential functionality of various microbial communities. Metatranscriptomics (studies of the transcripts from a mixture of microbial species) and other meta-omics approaches hold even greater promise for providing additional insights into functional and regulatory characteristics of the microbial communities. Current metatranscriptomics projects are often carried out without matched metagenomic datasets (of the same microbial communities). For the projects that produce both metatranscriptomic and metagenomic datasets, their analyses are often not integrated. Metagenome assemblies are far from perfect, partially explaining why metagenome assemblies are not used for the analysis of metatranscriptomic datasets.Results: Here, we report a reads mapping algorithm for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction k-mers (k-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph. We developed an application of this mapping algorithm: a reference-based approach to metatranscriptome assembly using graphs of metagenome assembly as the reference. Our results show that this new approach (called TAG) helps to assemble substantially more transcripts that otherwise would have been missed or truncated because of the fragmented nature of the reference metagenome.Availability and implementation: TAG was implemented in C++ and has been tested extensively on the Linux platform. It is available for download as open source at http://omics.informatics.indiana.edu/TAG.Contact:yye@indiana.edu äUtilizing de Bruijn graph of metagenome assembly for metatranscriptome(epmc).pdf DeepDyve Pubget Overpricing