Pub Date : 2018-06-01Epub Date: 2018-07-13DOI: 10.1007/978-3-319-94968-0_6
Tunazzina Islam, Desh Ranjan, Eleanor Young, Ming Xiao, Mohammad Zubair, Harold Riethman
It is currently impossible to get complete de-novo assembly of segmentally duplicated genome regions using genome-wide short-read datasets. Here, we devise a new computational method called Regional Extension of Assemblies Using Linked-Reads (REXTAL) for improved region-specific assembly of segmental duplication-containing DNA, leveraging genomic short-read datasets generated from large DNA molecules partitioned and barcoded using the "Gel Bead in Emulsion" (GEM) microfluidic method (Zheng et al., 2016). We show that using REXTAL, it is possible to extend assembly of single-copy diploid DNA into adjacent, otherwise inaccessible subtelomere segmental duplication regions and other subtelomeric gap regions. Moreover, REXTAL is computationally more efficient for the directed assembly of such regions from multiple genomes (e.g., for the comparison of structural variation) than genome-wide assembly approaches.
{"title":"REXTAL: Regional Extension of Assemblies Using Linked-Reads.","authors":"Tunazzina Islam, Desh Ranjan, Eleanor Young, Ming Xiao, Mohammad Zubair, Harold Riethman","doi":"10.1007/978-3-319-94968-0_6","DOIUrl":"https://doi.org/10.1007/978-3-319-94968-0_6","url":null,"abstract":"<p><p>It is currently impossible to get complete de-novo assembly of segmentally duplicated genome regions using genome-wide short-read datasets. Here, we devise a new computational method called Regional Extension of Assemblies Using Linked-Reads (REXTAL) for improved region-specific assembly of segmental duplication-containing DNA, leveraging genomic short-read datasets generated from large DNA molecules partitioned and barcoded using the \"Gel Bead in Emulsion\" (GEM) microfluidic method (Zheng et al., 2016). We show that using REXTAL, it is possible to extend assembly of single-copy diploid DNA into adjacent, otherwise inaccessible subtelomere segmental duplication regions and other subtelomeric gap regions. Moreover, REXTAL is computationally more efficient for the directed assembly of such regions from multiple genomes (e.g., for the comparison of structural variation) than genome-wide assembly approaches.</p>","PeriodicalId":92882,"journal":{"name":"Bioinformatics research and applications : 14th International Symposium, ISBRA 2018, Beijing, China, June 8-11, 2018, Proceedings. ISBRA (Conference) (14th : 2018 : Beijing, China)","volume":"10847 ","pages":"63-78"},"PeriodicalIF":0.0,"publicationDate":"2018-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-3-319-94968-0_6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37608405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-06-01Epub Date: 2018-07-13DOI: 10.1007/978-3-319-94968-0_22
Devin Haslam, Salim Sazzed, Willy Wriggers, Julio Kovcas, Junha Song, Manfred Auer, Jing He
Cryo-electron microscopy (Cryo-EM) and cryo-electron tomography (cryo-ET) produce 3-D density maps of biological molecules at a range of resolution levels. Pattern recognition tools are important in distinguishing biological components from volumetric maps with the available resolutions. One of the most distinct characters in density maps at medium (5-10 Å) resolution is the visibility of protein secondary structures. Although computational methods have been developed, the accurate detection of helices and β-strands from cryo-EM density maps is still an active research area. We have developed a tool for protein secondary structure detection and evaluation of medium resolution 3-D cryo-EM density maps which combines three computational methods (SSETracer, StrandTwister, and AxisComparison). The program was integrated in UCSF Chimera, a popular visualization software in the cryo-EM community. In related work, we have developed BundleTrac, a computational method to trace filaments in a bundle from lower resolution cryo-ET density maps. It has been applied to actin filament tracing in stereocilia with good accuracy and can be potentially added as a tool in Chimera.
{"title":"A Pattern Recognition Tool for Medium-resolution Cryo-EM Density Maps and Low-resolution Cryo-ET Density maps.","authors":"Devin Haslam, Salim Sazzed, Willy Wriggers, Julio Kovcas, Junha Song, Manfred Auer, Jing He","doi":"10.1007/978-3-319-94968-0_22","DOIUrl":"10.1007/978-3-319-94968-0_22","url":null,"abstract":"<p><p>Cryo-electron microscopy (Cryo-EM) and cryo-electron tomography (cryo-ET) produce 3-D density maps of biological molecules at a range of resolution levels. Pattern recognition tools are important in distinguishing biological components from volumetric maps with the available resolutions. One of the most distinct characters in density maps at medium (5-10 Å) resolution is the visibility of protein secondary structures. Although computational methods have been developed, the accurate detection of helices and β-strands from cryo-EM density maps is still an active research area. We have developed a tool for protein secondary structure detection and evaluation of medium resolution 3-D cryo-EM density maps which combines three computational methods (SSETracer, StrandTwister, and AxisComparison). The program was integrated in UCSF Chimera, a popular visualization software in the cryo-EM community. In related work, we have developed BundleTrac, a computational method to trace filaments in a bundle from lower resolution cryo-ET density maps. It has been applied to actin filament tracing in stereocilia with good accuracy and can be potentially added as a tool in Chimera.</p>","PeriodicalId":92882,"journal":{"name":"Bioinformatics research and applications : 14th International Symposium, ISBRA 2018, Beijing, China, June 8-11, 2018, Proceedings. ISBRA (Conference) (14th : 2018 : Beijing, China)","volume":" ","pages":"233-238"},"PeriodicalIF":0.0,"publicationDate":"2018-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9645795/pdf/nihms967636.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40490561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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