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10.1186/s12859-017-1678-9 http://scihub22266oqcxt.onion/10.1186/s12859-017-1678-9 C5437615!5437615 !28521770     free     free     free Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Warning: imagejpeg(C:\Inetpub\vhosts\kidney.de\httpdocs\phplern\28521770 .jpg): Failed to open stream: No such file or directory in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 117       BMC+Bioinformatics 2017 ; 18 (1 ): 263 Nephropedia Template TP {{tp|p=28521770 |t=2017. Coordinates and intervals in graph-based reference genomes |pdf=|usr=}}{{28521770 }} gab.com Text Coordinates and intervals in graph-based reference genomes JO: BMC Bioinformatics http://www.kidney.de/pget.php?&tw=1&pmid=28521770 #FOAvip BACKGROUND: It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represent genomic intervals, such as the positions of genes or transcription factor binding sites, on graph-based reference genomes. RESULTS: We formalize offset-based coordinate systems on graph-based reference genomes and introduce methods for representing intervals on these reference structures. We show the advantage of our methods by representing genes on a graph-based representation of the newest assembly of the human genome (GRCh38) and its alternative loci for regions that are highly variable. CONCLUSION: More complex reference genomes, containing alternative loci, require methods to represent genomic data on these structures. Our proposed notation for genomic intervals makes it possible to fully utilize the alternative loci of the GRCh38 assembly and potential future graph-based reference genomes. We have made a Python package for representing such intervals on offset-based coordinate systems, available at https://github.com/uio-cels/offsetbasedgraph . An interactive web-tool using this Python package to visualize genes on a graph created from GRCh38 is available at https://github.com/uio-cels/genomicgraphcoords . Twit Text FOAVip Coordinates and intervals in graph-based reference genomes ????BMC Bioinformatics http://www.kidney.de/pget.php?&tw=1&pmid=28521770 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=28521770 #FOAvip English Wikipedia <ref>{{Cite pmid|28521770 }}</ref> Coordinates and intervals in graph-based reference genomes #MMPMID28521770 Rand KD ; Grytten I ; Nederbragt AJ ; Storvik GO ; Glad IK ; Sandve GK BMC Bioinformatics 2017[May]; 18 (1 ): 263 PMID28521770 show ga BACKGROUND: It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represent genomic intervals, such as the positions of genes or transcription factor binding sites, on graph-based reference genomes. RESULTS: We formalize offset-based coordinate systems on graph-based reference genomes and introduce methods for representing intervals on these reference structures. We show the advantage of our methods by representing genes on a graph-based representation of the newest assembly of the human genome (GRCh38) and its alternative loci for regions that are highly variable. CONCLUSION: More complex reference genomes, containing alternative loci, require methods to represent genomic data on these structures. Our proposed notation for genomic intervals makes it possible to fully utilize the alternative loci of the GRCh38 assembly and potential future graph-based reference genomes. We have made a Python package for representing such intervals on offset-based coordinate systems, available at https://github.com/uio-cels/offsetbasedgraph . An interactive web-tool using this Python package to visualize genes on a graph created from GRCh38 is available at https://github.com/uio-cels/genomicgraphcoords . |*Computer Graphics [MESH] |*Genome, Human [MESH] |Algorithms [MESH] |Genetic Loci [MESH] |Genomics/*methods [MESH] |Humans [MESH] |Internet [MESH] |RNA, Messenger/genetics/metabolism [MESH] |Sequence Analysis, DNA [MESH]Coordinates and intervals in graph-based reference genomes (epmc).pdf DeepDyve Pubget Overpricing