The fast development of next-generation sequencing technology presents a major computational challenge for data processing and analysis.A fast algorithm,de Bruijn graph has been successfully used for genome DNA de nov...The fast development of next-generation sequencing technology presents a major computational challenge for data processing and analysis.A fast algorithm,de Bruijn graph has been successfully used for genome DNA de novo assembly;nevertheless,its performance for transcriptome assembly is unclear.In this study,we used both simulated and real RNA-Seq data,from either artificial RNA templates or human transcripts,to evaluate five de novo assemblers,ABySS,Mira,Trinity,Velvet and Oases.Of these assemblers,ABySS,Trinity,Velvet and Oases are all based on de Bruijn graph,and Mira uses an overlap graph algorithm.Various numbers of RNA short reads were selected from the External RNA Control Consortium(ERCC) data and human chromosome 22.A number of statistics were then calculated for the resulting contigs from each assembler.Each experiment was repeated multiple times to obtain the mean statistics and standard error estimate.Trinity had relative good performance for both ERCC and human data,but it may not consistently generate full length transcripts.ABySS was the fastest method but its assembly quality was low.Mira gave a good rate for mapping its contigs onto human chromosome 22,but its computational speed is not satisfactory.Our results suggest that transcript assembly remains a challenge problem for bioinformatics society.Therefore,a novel assembler is in need for assembling transcriptome data generated by next generation sequencing technique.展开更多
Two new different Cu(Ⅱ) MOFs with the same 1,3,5-tris(1-imidazolyl) benzene(tib) ligand {[Cu(tib)2]·(H2O)2·Br2}n(1) and {[Cu2(tib)·Br·Cl]·2Br}n(2) were obtained by one pot synthesized of tib ...Two new different Cu(Ⅱ) MOFs with the same 1,3,5-tris(1-imidazolyl) benzene(tib) ligand {[Cu(tib)2]·(H2O)2·Br2}n(1) and {[Cu2(tib)·Br·Cl]·2Br}n(2) were obtained by one pot synthesized of tib with CuBr in the presences of HCl and water. X-ray single crystal diffraction analyses indicate that both complexes 1 and 2 have two dimensional frameworks containing different building blocks. Each Cu(Ⅱ) atom in complex 1 is coordinated by four N atoms from different tib ligands. However, there are two different cryptographic Cu(Ⅱ) atoms in complex 2, one is four coordinated by two bromine atoms and two N atoms from different tib ligands, the other is six coordinated by two chloride atoms and four N atoms from different tib ligands. The thermal gravimetric analysis of complexes 1 and 2 are depicted in the paper.展开更多
基金supported by grants from the National Center for Research Resources (5P20RR016471-12)the National Institute of General Medical Sciences (8 P20 GM103442-12) from the National Institutes of Healththe seed collaborative research grant from the Odegard School of Aerospace Sciences and the School of Medicine and Health Sciences at University of North Dakota
文摘The fast development of next-generation sequencing technology presents a major computational challenge for data processing and analysis.A fast algorithm,de Bruijn graph has been successfully used for genome DNA de novo assembly;nevertheless,its performance for transcriptome assembly is unclear.In this study,we used both simulated and real RNA-Seq data,from either artificial RNA templates or human transcripts,to evaluate five de novo assemblers,ABySS,Mira,Trinity,Velvet and Oases.Of these assemblers,ABySS,Trinity,Velvet and Oases are all based on de Bruijn graph,and Mira uses an overlap graph algorithm.Various numbers of RNA short reads were selected from the External RNA Control Consortium(ERCC) data and human chromosome 22.A number of statistics were then calculated for the resulting contigs from each assembler.Each experiment was repeated multiple times to obtain the mean statistics and standard error estimate.Trinity had relative good performance for both ERCC and human data,but it may not consistently generate full length transcripts.ABySS was the fastest method but its assembly quality was low.Mira gave a good rate for mapping its contigs onto human chromosome 22,but its computational speed is not satisfactory.Our results suggest that transcript assembly remains a challenge problem for bioinformatics society.Therefore,a novel assembler is in need for assembling transcriptome data generated by next generation sequencing technique.
基金funded by the National Natural Science Foundation of China(21261009)Young Scientist Foundation of Jiangxi Provincethe Education Fund of Jiangxi Province(GJJ13434)
文摘Two new different Cu(Ⅱ) MOFs with the same 1,3,5-tris(1-imidazolyl) benzene(tib) ligand {[Cu(tib)2]·(H2O)2·Br2}n(1) and {[Cu2(tib)·Br·Cl]·2Br}n(2) were obtained by one pot synthesized of tib with CuBr in the presences of HCl and water. X-ray single crystal diffraction analyses indicate that both complexes 1 and 2 have two dimensional frameworks containing different building blocks. Each Cu(Ⅱ) atom in complex 1 is coordinated by four N atoms from different tib ligands. However, there are two different cryptographic Cu(Ⅱ) atoms in complex 2, one is four coordinated by two bromine atoms and two N atoms from different tib ligands, the other is six coordinated by two chloride atoms and four N atoms from different tib ligands. The thermal gravimetric analysis of complexes 1 and 2 are depicted in the paper.
